Every time I have prebaked the squash, it did cook considerably, yes. The recipes were things like soup recipes, which (like your recipe called for uncooked squash. I just revised the cooking time accordingly (to take into account the baking) and have never had a problem with the flavours not melding or anything, or with the squash being overcooked. Good luck!
"If you're not chasing after miracles, what's the point?" The movie Saint Ralph
"What it all comes down to
Is that everything's gonna be fine fine fine
I've got one hand in my pocket
And the other one is giving a high five" - Alanis Morisette, Hand in My Pocket