Ohhh... the luxury. If you have an active grille shutter system, then you have no worries doing whatever the hell you want to the engine bay. The radiator system will adjust automagically.
Belly pan holes are for multiple reasons: water drainage, debris clearing, servicing, visual inspection, aero, airflow, and resonance. Unless it's a choppy, flimsy piece of junk, you are probably better off not touching it. Some of the holes are probably there for exotic cases we don't normally think about, like sloughing snow from the engine compartment after driving through a drift or somesuch. Just my two sense.
Yah, Killmat made a huge difference when I put it in my car, especially the doors, wheel wells, spare wheel well, and engine wall. I also put some insulation in my doors when I did the Killmat, for exactly the same thermal leakage reason. Actually, I insulated the whole car, just for the comfort aspect.
If you do the insulation on the roof, consider adding a reflective radiant barrier first (with a gap), then normal resistive insulation underneath. It makes a -5F difference on a hot 90F day. I also painted my roof white, which while garish, also cools by -3F on a hot day (from a gray color). It would have a bigger delta from a black. I hear they make IR reflective paints nowadays, so that could also be an option if one wants both heat reflectance and aesthetic beauty. Personally, I don't care for the latter.
