Does microwaving fully cook chapatis?
I have made chapatis many times, although I'm not an expert by any stretch of the imagination. Most of my attempts have come out just fine.

Chapatis/rotis are usually cooked on a tava (or tawa) - which is basically a flat or slightly concave cast iron pan. A flat griddle pan or even a frying pan(skillet) could be used instead.

I've also seen them cooked over an open flame, but this is certainly not necessary.

I wouldn't recommend microwaving chapatis to cook them.  They won't get the brown spots of colour or develop the same flavour caused by toasting of the surface. They will likely end up being tasteless cooked lumps of dough.

If you are talking about store-bought chapatis, then these are already cooked. If you want to reheat them, you could do it in a microwave. I would sprinkle with a little water first and wrap them in a dish towel, and microwave for 20 seconds or less until just warmed.  I guess you could also reheat them in a dry pan, but not too long or they will just dry out. Again sprinkling with a little water might help them not dry out.