Some protocols (metabolomics) use boiling methanol for metabolites extraction and cleaning glassware. Is it safe to boil methanol in a microwave?
It is possible and is not unheard to perform an extraction assisted by microwaves (even "dry ones" e.g.). Either you seal the reaction vessel with a special cap to clamp, and monitor temperature and pressure evolution in function of time and power applied by the dedicated microwave oven. This has the potential advantage of both rapid heating, and "pressure cooking". (Depending on the material, using the reaction tube sealed a twice may be discouraged, though.)
Or you opt-in for a system where the the reaction flask is in the microwave oven, and the reflux condenser passes across the walls of the oven. While in principle ovens designed for use in a kitchen may be used, e.g.,
it is both safer and more reproducible to use ovens dedicated to this (especially: focussing on the spot where your reactor is situated) and providing proper shielding and monitoring of the process parameters.
Methanol flashpoint is listed as 11 °C to 12 °C (52 °F to 54 °F), upper flammable limit is listed as 36%, so it seems likely that it could enter into a flammable limit.
Also you may need to understand heat input/vaporization rate vs vent path through your condenser.
I too think a “home built” microwave setup does not sound safe.