Update: I got my visa no problems. Went at 9am and they said it's no problem I was a day late, just to come back at 1:30-3pm.
I'm guessing it's different from Vientiane bc 1) I paid upfront when submitting the documents, and 2) the Thai embassy in Myanmar isn't a visa factory for foreigners, so it is far easier to deal with the occasional forgotten passport.
Just FYI, in case anyone finds themselves in a similar situation.