Well, I might be able to add some input here w/ regards to wires & "holes".
When I had the carpet up in my 318ic recently, the floor pan has metal "plugs" in it which are sealed by factory body sealant. There is one in the center of each of the floor pans (L front, R front, L rear and R rear). Obviously if these plugs were removed, you would have holes in the floor pans.
As for wiring, all of the wiring runs from front to rear down the L & R interior rocker walls and is held into place via factory reusable plastic "zip ties". I had my rear seat completely out and the carpet lifted up on each side of the center trans tunnel and I did not see any wiring running down the middle of my vehicle. The ONLY wires that branch off of the rocker harnesses are those that go to each front seat, but are secured to the floor as well. All of the wires from the firewall & kick panels run right along the rockers and it's tucked pretty tight against the rocker wall since it's all secured via the factory zip ties. Even w/ the back seat completely removed, you don't see any wiring harnesses because they are tucked under the rear interior 1/4 panels.
Now, in my 318ic, I also have black plastic covers that mount over the rockers & carpet (I'm assuming these exist in the coupes & sedans as well) - IF the carpet is removed and these rocker covers are reinstalled, these rocker covers will hide most of the exposed wire loom against the rockers. So, if retaining your front kick panels, rocker cover panels and the rear interior 1/4 panels, I don't think you're going to see much exposed wire or harnesses at all. The only wires you may see would be the ones that branch from the rocker to under the front seats (and even then you won't see much of those, because there is only like a 1-2" gap from the face of the rocker wall to the side of each front seat).
I've also seen some folks who do "gut" their interiors get the floor pans coated in the same substance as "Rhino Liner" as used for truck bed liners. This makes the bare floor surface more uniform while at the same time, it reduces NVH and the floor is also protected against rusting. I've seen this done on many types of vehicles and it's not expensive to do either.