Interesting answer from blorg on https://redd.it/g4n057:
The official answer is national security concerns, and whether they are valid or not, that probably is the motivation. There is a substantial segment of the government here that wants to keep foreigners on a very short leash.
Just look at how visa regulations have been tightened up over the last five years or so, although I'm not speculating based on that, they have explicitly said it is national security concerns.
https://www.bangkokpost.com/opinion/opinion/1888015/end-tourist-paper-chase:
Bureau deputy spokesman Phakkhaphong Saiubon insisted that online applications are not allowed for this group of foreigners due to national security concerns.
During a national health crisis, the bureau's treatment of this group of foreigners should have been much better.
Apart from the need to be sensitive to their genuine fears of infection in a foreign country, the bureau should not forget that tourism has been the backbone of the country's economy for a long time. Tourism contributes about 20% of GDP, and last year the country earned 1.96 trillion baht from its 39.8 million visitors.
National Security has become a catchphrase used by the bureau in recent years whenever it faced criticism over irrational policies towards foreigners. These include an odd measure to have them report any changes of residence, even temporary, within 24 hours.
If the bureau is concerned about national security, it should rely on strict, specific screening and surveillance to target particular criminal suspects rather than counterproductive blanket measures.
As the virus continues to spread unabated, the bureau should let tourists extend their visas online. At the moment, it is Covid-19 that is posing a national security threat -- not stranded tourists.
Update (2020-04-21):
Foreigners whose visas had expired since March 26 will be permitted to stay until July 31 without having to apply for an extension, said Narumon Pinyosinwat, spokeswoman for the Thai government.
so it seems the Thai government agreed that it makes sense to give a longer extension.