I have on oem size spare on a 15' stock rim and the tire seems to sit high and there for the front of the cover wont sit flat? is the spare a smaller size than the 165
/80 15?Click to view attachment

Seems the front is up on a ledge

Is the floor pushed up from an impact in the tow hook area?

Looks good. Some small dents. Compared to online phots and looks same.

Mine has been this way as long as I've owned it. 4-lug Mahle wheels (including the spare).

Mine is the same. Drives me crazy, but I think that's how it is. I have steelies.

Mine is the same, just the way they are.

Yep, me too. My trunk floor is perfect. I mounted a 195 tire on my Fuchs 4-spoke spare and it was really horrible. Swapped that for a 165 and the cover board still rides high - acceptable, but annoying. Might have to try a 155 and see how that works.

It does look like a floor jack was used under the middle of the floor.
It probably doesn't cause your problem but can easily be fixed.
Stand in the center of the floor with feet together.
You'll probably feel it drop a bit.