I'm sure you have sprayed many metallic pieces off the car and all was well. I have done this many times in the past and if I was painting the car I would paint it in pieces. I have also shot Tri stage liquid crystal, blue base, with transparent orange over top in pieces, a deep green base with radiance green over top, all in pieces...the last one was over 1000 pieces shot seperately and it all worked out fine. You, as I, obviously have experience in painting. We understand, air pressure, temperature, reducer grade, (fast, medium, slow) distance from the panel, gun set up, drop coat, volume of paint...as you know, these will all have an effect on color in metallic's and varying some or any of these can change the lightness or darkness of the color. It is a common practice for experienced painters in collision shops to make gun adjustments to match factory colors in metallic's. Many people who post here don't have this knowledge that comes from the experience that over years of painting, we have had the fortune to garner and are asking us as professionals for help.
When these people post, I try to help them in the simplest way for them to get the best results, especially if they don't possess the years of experience it has taken me to enable me to do a tri stage in pieces. I'm not saying it can't be done...it can, but, The first engine I built didn't run 9's in the quarter mile, I didn't know enough as to how to build it, tolerances, matching parts, the importance of balancing, porting, polishing, suspension and so on...and I still have a lot to learn in this regard and there are a host of people on this site that would run circles around me. I'm learning.
If a person posts and has a question as to should he spray his windshield channels and install his glass before he paints the rest of the car and is afraid of scratching when assembling the pre painted pieces tells me that the experience that others may have is not present here and is asking a question not as to "can it be done" more to, "do I have to or should I or what is the easiest way to get an acceptable result with minimal potential for problems. Body Shops don't remove the windshield to paint a roof.
Lets look at the alternative, what if a person painting with minimal experience is painting a silver car in pieces and all we tell him is "I have done plenty of metallics apart without any vary at all. Have even shot the doors laying down a few times, instead of hanging them the way they would end up on the car", and the person sprays the car in pieces over several days and somewhere in the process the pressure on his gun varies by 4 pounds, or he changes the volume of paint coming out or whatever, conditions are not the same. Will the color be the same? In metallic's the correct answer is a flat out NO! If you paint a car in a solid color, you can virtually use a garden hose and a vacuum cleaner and the color will remain the same, not true with metallic's.
NovaFreak gave the original post great advice about taping edges so as not to scratch when assembling a vehicle painted in pieces and this is the type of advice that I feel should be given. Consider this, if the OP new what you new he wouldn't be posting, correct?
I've seen your work and you are an excellent painter and please don't be offended by what I'm posting, I'm trying to keep it as simple as possible so the OP can get the experience and confidence in the future, that we have now and to not even think about should I or shouldn't I paint the windshield channels before I paint the entire car.
Sorry for being long winded, but I needed to explain why I try and keep it simple and pass on the knowledge that has taken me over 30 years to attain then simply say NO PROBLEM.
Ray