Either way will certainly work, Larry. But my vote also goes to just laying it up directly on the windscreen. There's a reason Vans recommends doing it that way. I would guess most of the vast number of RV's that are finished and flying were done Vans' way.
Advantages, as I see it:
Structural strength. If you do the layups directly on the windscreen, in place, you'll avoid drilling all those unnecessary holes in the plexi. Even though you'll fill them later, I still see a risk of cracking, either now or later. And what about the final structural strength of a windscreen shot full of holes? Even though they're filled, is that as strong as an undrilled one?
You're going to use proseal? Really? Is that as strong as bonded layups? I would at least be considering the question. Along with the effects of temperature changes. Expansion, contraction. The pressure of the windblast on the windscreen. I'd want mine firmly bonded in place, and I wouldn't want holes in it either. JMHO
Speaking of holes, you may not like the appearance of your fairing from inside your cabin when you're finished. Remember, you'll see through the plexi from the inside. Every time you climb in and sit down, you're looking at the back side of your fairing. And even though you fill those holes, you'll see every one of them from inside. You may not have thought of this because it's not an issue with the rear fairing.
Less work. Again, JMHO, I've only built one. I do think you're overthinking this.
A fairing finished in place can be finely finished to fit so well, the smooth transition is unmatched. When it's painted you won't even see it. Just my opinion, I've only done one. It's not that hard. If you mask off the plexi with a piece of electrical tape and sand down to the tape, when you pull it off you'll have an edge so thin it will hardly catch your fingernail. And on the forward edge, you feather it out so you can't even see it when it's painted. There's no way to match a fit like that building it on the bench. You can see how mine turned out. I'll put in a picture here. Mine's a tip-up, but the ideas are the same. It's not that hard. I had never done this before.
Either way you go, good luck with it. I looked at your website and I'm very impressed with your work!