I have built a 32 meter tall tower, and do not experience a micro climate inside the building, but then again it is not as large, and is stone. However I do get snow on the top when the tower is in the meadows. This has a thatch roof about 8 m above it, and that functions as you would expect.

I have built a 22m tall stone tower, with a thatch roof and the thatch, though snow covered behaved perfectly normal in mountains.

I have built towers that span two biomes, and again, everything works exactly as expected.

So I can not offer any advice on limits, and as you say you have to go 40m up before the roof functions correctly, i.e. only 12m above your head or so. I have a 25m high atrium, and that works.

So pics please as it sound like you have multiple issues here.