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Essentially all the federal agencies have control over their spending. The DOT can raise revenue by road tolls, DOE has royalties, Medicare/ss can garnish small amounts of wages that aren't worth fighting in court, USDA/other agencies has tariffs and inspection fees, HUD has rents, Dept. ed has loans, military has arms sales, science and foreign affairs are basically military, etc.
Is there any situation where the Congress or president would have any control over government spending?
You said
The DOT can raise revenue by road tolls
See USA Today
The 1956 Interstate Highway Act generally bans tolling on interstates.
The Department of Transportation cannot add tolls on its own. It would need congressional authorization.
You said
Medicare/ss can garnish small amounts of wages that aren't worth fighting in court
There is a thing called a class action suit, where small amounts can be aggregated into large amounts so as to make them "worth fighting in court". Medicare and Social Security combine for a 15.3% tax on income and almost half of federal government spending. They are the two largest federal programs with Defense a distant third. Any amount small enough to not be worth fighting on an individual basis isn't going to make much of a difference in their budgets either.
You said
DOA has tariffs
Department of Agriculture? It does not have tariffs, and the agency that does can't change them on its own.
HUD has rents
Mostly Housing and Urban Development subsidizes housing built and operated by states and localities. I believe that you will find that HUD has very few properties of its own on which it can charge rent.
Dept. ed has loans
Sure, the Department of Education has loans, but they are constrained by law to operate a certain way, and that way is not profitable.
military has arms sales
Mostly military suppliers have arms sales. The military itself generally sells surplus at a loss rather than new arms at a profit.
science and foreign affairs are basically military
While there is considerable military-funded research, there is also government civilian-funded research. And the Department of State would be quite surprised to find that they are part of the military. And the military would be surprised too; doubtless they will want to make a lot of changes when they discover that. There may be a sense in which that is true, but that sense is not budgetary.
Is there any situation where the Congress or president would have any control over government spending?
Well, considering that the president appoints the people who run all these departments and can give them orders, any flexibility that they do have is under presidential control. So yes, the president certainly has some influence.
Beyond that, Congress sets the laws under which the departments operate, including their budgets. Further, none of these departments is self-funded. They all need subsidized by the general funds (except possibly Transportation and Treasury).
The federal government is needed to redistribute funds between departments. While most federal departments do have some minor forms of income, for most of them the income does not nearly cover the cost. The only federal department which generates a surplus is the department of treasury, which collects taxes through the Internal Revenue Service. The federal budget then redistributes this surplus on the other departments.
For most departments, covering all of their own costs is simply not realistic.
The federal government is needed to legitimize the departments. When there were no government, who would say that the Department of Health is the department of Health? Why can't someone else form their own Department of Health, publish health regulations and enforce them with force of law? When the different departments publish regulations which contradict each other, which should I follow? That's why there is just one Department of Health. Because the government says so, and the final decision maker in its matters is the current Secretary of Health because the government appointed him.
The federal government is needed to regulate the departments. The rights and duties of every department are determined by laws. The government makes these laws and changes them when circumstances change. When a government department writes you a check or charges you with a bill, they do so because a law says they can/should/must do this in this situation. When you disagree with their interpretation of the law, then you have the right to appeal their decision. But if it turns out the government agency is acting within the law, that appeal won't be successful. But without a government making laws for them, the departments either couldn't do anything (which means they could not fulfill their purpose) or they could do whatever they want (opening the door to arbitrariness, corruption and eventually despotism).
The anarcho-capitalists or extreme libertarians might question whether the United States need any government departments at all and if it wouldn't be better if all the services currently performed by government departments would be left to self-regulating free markets. But that is not the system the United States works under right now. In fact no modern country has ever attempted to implement such a system (at least not in a controlled manner: failed states which recover from a civil war often go through a period of anarcho-capitalism until a new government established itself).
I am not claiming that the US system is flawless in every detail or even the best possible system for the US could be working under. But if you compare the median standard of living of the US with that of other countries, then something seems to be going right there.
Whether anarcho-capitalism could work even better for the United States or not is a mostly theoretical debate which is better left to more debate-oriented websites.
