Nah, not a waste in my opinion. Sure, it'll cost you a small amount extra for the foam that you'll eventually remove and discard. But, you won't have to worry about foam accidentally getting onto your beautiful brand new windows! The pros that spayed my bus did a very thorough job of masking, but I still ended up scraping concrete-like foam off of 1/2 the windows, and there are a few trim pieces that I'll never get it off of.
Just don't do what I did and try to mask off where you're windows will eventually go. I masked off where I guessed my roof vents would go and it worked fine, but was definitely wasted effort. Should have just foamed everywhere and cut out holes later like you're suggesting.
Oh, and one more suggestion: embed your favorite type of flexible conduit into the roof foam, crossing the bus from one side to the other. I wish I had done that - I've already outgrown my initial wiring plan and now have to route wires under the bus.