How much would your painter charge per window? Will he do as good of a job as a factory finish done inside a conditioned shop? For $76 I would have them factory painted, in my opinion that is cheap.

It is much less expensive to have the factory do it but be aware that it is a sprayed finish and wood grain will be "visible". The parts are sprayed and then assembled in the window. If you are super picky (and you know who you are), I would have a job site painter do it or use the factory paint as a primer. Also, remember some "touch up" may be needed and that will up to the builder. By "touch up", I mean minor scratches and dings that occur on site not prior to delivery.

The factory does a better job on the muntins than a job site painter in regard to the "drips" that can be seen when you are on the outside of the window looking at the backside of the interior muntin. Small detail but can be very important.

is it possible to just have the muntins painted at the factory, and everything else primed (then painted on site)? What is your recommendation?

For $76, I would have the entire window painted and see if you are happy with that. As I said earlier, you can use the factory finish as a first or prime coat.

The factory finish is undoubtedly worth it, and provides a significantly more controlled environment (compared to a house) in which to paint.

+1. Put me the factory finish camp as well.