The problem is exactly public data accuracy, disclosure, and transparency, as you stated in the title.
With the data coming into the CDC, there's little to no politicization of the data. (At least there's not supposed to be, since it's not a political organization.)
With the data going to the White House, it can potentially be manipulated before it goes to the medical organizations that need it for forecasting as well as public reporting. There's already been a problem with the public reporting of the data.
On the eve of a new coronavirus reporting system this week, data disappeared from a Centers for Disease Control and Prevention website as hospitals began filing information to a private contractor or their states instead. A day later, an outcry — including from other federal health officials — prompted the Trump administration to reinstate that dashboard and another daily CDC report on the pandemic.
And on Thursday, the nation’s governors joined the chorus of objections over the abruptness of the change to the reporting protocols for hospitals, asking the administration to delay the shift for 30 days. In a statement, the National Governors Association said hospitals need the time to learn a new system, as they continue to deal with this pandemic.
The governors also urged the administration to keep the information publicly available.
The perception here is that the removal of the data was on purpose, presumably in an effort to make the numbers agree with what Trump says. With the governors believing that with Trump's administration compiling the data, it can do whatever it wants to with the data before letting anyone else see it.
Politico reports that the data was taken down by the CDC, stating they believe they should be the originator of the compiled information, not the White House.
After the Trump administration ordered hospitals to change how they report coronavirus data to the government, effectively bypassing the Centers for Disease Control and Prevention, officials at the CDC made a decision of their own: Take our data and go home.
The flap over the missing CDC data is just the latest source of tension between the CDC and federal health officials that’s contributed to a fragmented response to the pandemic. CDC officials have complained they’ve been unusually sidelined during the crisis as President Donald Trump pushes for faster reopenings, while White House officials contend they’re being forced to work around the agency’s weak spots.
The new system the White House has seems to be full of problems, though, even when it's touted to be better than the CDC's system.
Instead, the public data hub created under the new system is updated erratically and is rife with inconsistencies and errors, data analysts say.
Hospitals are supposed to report daily to the federal government how many beds they have, the number occupied and the availability of intensive care beds. Under the new system, the Department of Health and Human Services aggregates the information at a state level and shares a daily spreadsheet of the information that has been reported — gaps and all.
But the old CDC approach interpreted the data a step further. CDC posted estimates derived from the data to show an approximation of the actual availability of ICU beds, accounting for the lags and gaps in reporting. These estimates — promised on the HHS website — have not been updated in over a week.
By contrast, the CDC estimates was updated three times a week. And while the data sent to CDC was vetted for accuracy before being posted publicly, the data sent to the new platform appears to be posted as it is received and contains multiple anomalies, analysts note.
So, for your first bullet point of the data being used differently than the old system: yes, no, and sort of-maybe. The new system is supposed to have improvements over the old system, but it's proving to have more problems. That's to be expected of a new piece of software, but it should have been rigorously tested before used in this way (speaking as a software dev). The new system was developed by an "unproven contractor", so there's no real telling if the system has the sort of historical experience in dealing with pandemics or medical data that the CDC's system does at this point. Only time will tell the real story, and that might be difficult by not having a (public or semi-public) secondary system to double-check the data.
Most of us remember how Trump infamously doctored the map of the path hurricane Dorian was supposed to take, with an extra loop over Alabama in Sharpie. Trump had earlier said Dorian was supposed to hit Alabama and this was used to "prove" his assertion. With this, and other, history of Trump and his administration modifying data to fit their agenda, it's no wonder that people, local and state governments, medical organizations, and others are wary of the possibility of modification of the data for political gains.
In an Oval Office briefing, Mr Trump pointed to a National Oceanic and Atmospheric Administration's (NOAA) forecast map from 29 August.
The chart had a black loop marked around Alabama that was not on the original version from last week.
Mr Trump told reporters that Dorian "would have affected a lot of other states".
Later on Wednesday at a White House event, when asked about the map discrepancy, Mr Trump offered no explanation. "I don't know," he said.
It began on Sunday morning when Mr Trump tweeted: "In addition to Florida - South Carolina, North Carolina, Georgia, and Alabama, will most likely be hit (much) harder than anticipated."
Twenty minutes later, the National Weather Service tweeted from Birmingham, Alabama, contradicting the president.
The same day, NOAA spokesman Christopher Vaccaro made clear in an email to reporters: "The current forecast path of Dorian does not include Alabama."
In fact, there's even an article from 2016 that has concerns about Trump's administration altering government data. This was before Trump even took office when the evidence of his potential to change things for political or personal opinion began to be noticed.
Certain steps being taken by the president-elect’s transition team have raised alarm bells for some who worry that Trump’s glibness with the truth could take root in a more institutional form. Trump’s nominee for EPA administrator, Scott Pruitt, is a climate change denialist. His choice for director of the National Economic Council, Gary Cohn, once called the U.S. employment rate “a very, very fictitious rate.” And last week, Bloomberg reported that the Trump transition team sent a memo to the Department of Energy requesting the names of employees involved in determining climate change metrics and asking the Energy Information Administration “in what instances the EIA’s independence was most challenged over the past eight years.”
What does have observers worried are two things in particular: budget cuts that could significantly affect data collection and quality, particularly within the government’s statistical agencies — those that produce key economic indicators like the Bureau of Labor Statistics and the Bureau of Economic Analysis; and the willful miscommunication of scientific research that proves politically inconvenient to the White House.
For your second bullet point, this report for 2015 says that reporting data to the CDC is voluntary, but laws may have changed since then. I can't find anything about it, but I don't have the time to look into it further.
Reporting laws vary by state regarding which diseases must be reported, who must report, whether case laboratory specimens must be submitted, and other features.1–5 This variation could affect a national public health response to a public health emergency, because federal health officials rely on voluntary reporting of epidemiological data from states to the Centers for Disease Control and Prevention (CDC). The recent outbreaks of Middle East respiratory syndrome coronavirus in the Arabian Peninsula and H7N9 influenza in China highlight the risk of emerging infectious diseases.6 A previous study found that some jurisdictions needed to revise inadequate reporting rules for bioterrorism agents.7 If a new infection with characteristics of ease of spread and high pathogenicity emerges, it is critical that every state have the legal authority to collect information to characterize the threat and effectively respond.
CDC relies on a variety of systems to monitor influenza, including hospitalized case reporting, syndromic surveillance, outbreak reports, overall mortality, and respiratory virus laboratory testing.8 During the 2009 H1N1 influenza pandemic, rapid collection of information on individual hospitalized cases was critical to understanding the nature of the new strain of influenza, the severity of illness it caused, and who was most at risk for infection and severe outcomes, including death.9,10 Risk factors emerged that were different from those associated with seasonal influenza, including pregnancy, obesity, American Indian/Alaska Native ethnicity, and younger age.11,12 However, not all states had the ability and resources to collect information on every case, even severe cases, and CDC needed to make extrapolations and estimates.5
And for your third bullet point, it might be that there's voluntary reporting, but the CDC lists cases of Covid-19 from all 50 states and 8 other provinces/protectorates/jurisdictions//etc., so it's safe to say that reporting is widespread and there's some list of who all is reporting, but I don't have the time to look for it. The map allows you to click on states to get more detail. There's also a section to look at data by county, which also has interactive maps to click on for more information. It seems to get pretty specific with the data, but I haven't yet found information for specific hospitals or testing sites.