Before cutting the floor, why don't you try to what you are suggesting, drop the crossmember or make a thinner mount, use some angle shims to adjust the pinion angle to match and see what happens? Easier than cutting the floor, and easier to undo. I think you may be just fine doing it that way. The driveline angles might not be perfect, but as long as the trans angle matches up to the pinion angle under load, you should be fine. You can always cut the floor later if it doesn't work out.
