I'm back in! On arrival I had to download the AOT app and submit a TM-8 form via this app. Afterwards you have your temperature check and proceed to immigration as normal. Bangkok airways currently do not ask for a med cert and insurance, unlike AirAsia. However this may change at any point. Good luck to anyone in the same situation.
Update: Successfully checked in with only a temperature check required. No health cert or insurance required as of now for Bangkok Airways. Heard rumours of AirAsia requiring these documents already even though the new rules are not meant to be in effect until the 22nd March
Arrived in Mandalay. Had pictures taken of my passport, visa and health declaration form which everyone needed to fill out on the flight. Return flight to Chiang Mai is at 8pm so I'll report back. So far no difficulties.