Do I need to remove some paint under the lid then or just not at all?
I've never needed to.
Remember, NMO's are designed to be installed "blind", as in going through the roof of the vehicle where you cannot necessarily get to the other side. The cable side of the NMO mount has teeth on it that are designed to bite into the sheet metal when tightened down.
It certainly won't hurt the antenna mount to do that.
I can slide them a little closer to get away from the side edges but it will still be 5 inches from the front edge and about the same from the back edge. I don’t expect much of an overload problem since I’m not one to talk too much on the radio but if I do end up talking a lot I could always install a coaxial relay to disconnect the scanner antenna (or maybe find a way to automate it).
Yeah, you are going to need to just deal with the fact that they won't be in an ideal location. As long as you accept that there will be some impact to performance (probably slight). You don't want them much closer.
I’m avoiding the top because I will be putting a temporary CB antenna up there sometimes, plus if I ever decide to play with mobile HF radios (the multi band style), their antennas are designed for trunk mounting.
The CB antenna will have less of a problem mounted on the trunk. It's long enough that the little bit of tinted/defroster window bits won't be an issue. I'd suggest considering putting the dual band antenna on the roof, dead center. The CB antenna can still go up there, or on the trunk.
The rear window has aftermarket tinting, so I don’t think that’s a problem, but there are some defroster wires.
It depends on what material they used. If there is any sort of metallic content, it'll impact things.
Also, having an antenna running 50 watts VHF and/or 35watts UHF that close to any rear seat passengers is not ideal. Putting it on the roof would be safer.
4 watts from a CB won't be an issue.
I’ll have to probably buy a new hole saw then. Mine are for wood.
If you expect to be doing this more than one or two times, investing in the right tool for the job can be a good idea.
However, in a pinch, these will work just fine:
https://www.amazon.com/DEWALT-D1800...24370637&sr=1-2&keywords=3/4"+hole+saw+dewalt
Plus, you can find them at Home Depot and other hardware stores. I had to do an install and I didn't have the right one, so I was able to run by Home Depot, pick one up and complete the job. It was on an aluminum body Ford, too.