Can I enter Thailand on a short-term visa and apply for an O retirement visa while already holding an OA visa?

Shouldn't affect you at all. Keep in mind in Chiang Mai you need a MINIMUM of 21 days to apply for an in country Non-O visa at the immigration office.

SO coming in on a 30 day visa exempt entry you're gonna cut it close trying to pull it off without getting the 30 day extension for 1900baht too

I think you're using the wrong abbreviation as well, an STV is a Special Tourist Visa (and is NOT what you want)

You should get a single entry tourist visa from the thai consulate when you're in Hong Kong and come back that way. That stamps you in for 60 days and you will have plenty of time to get the documentation together to apply for the in country 90 day Non-O for 2000baht and then once you get that you will apply for the year extension when you have 45 days or less left for 1900baht