front and rear glass installation

yeah, it's kind of a catch-22. The paint job will be better (marginally, imho, in the case of front and back glass, because the moldings will cover the paint edge, but still better) if you can do it with everything out, but then you run the risk, like you say, of causing scratches putting it back together.

I'm not sure if your back window uses a lockstrip or not (mine does)- if not, they can probably be roped in, and then there should be very little risk of paint damage during the process.

In some cases sealant isn't actually required, but in my experience most guys use something for a sealant anyways- better safe than sorry.