Ask yourself what your goal is and how you think you'll use the truck over the coming years. I find myself moving a variety of things and sometimes a spray-in bedliner is helpful, other times a big pain. Say for example if I need to move something large, heavy, and to a degree fragile - furniture or an old arcade game/pinball machine, slide that across spray-in bedliner and it beats up your item. Got to put something else down on top of the bedliner first.
I like the rubber bed mats, and I had one in my '94 C2500LD. Didn't have any trouble with it collecting moisture as it has a whole ocean of raised dimples underneath so there was some separation between the bed floor and the underside of the mat. The few times I lifted it up, never saw any damage.. EXCEPT.. those dimples beat into the paint over the years. So, freshly painted (or nice original paint) bed? Not sure I'd put a bed mat in there. Paint already beat up from use? No worries.
And plastic bedliners are pretty much useless "dress-up" items, IMO. You can't put anything back there without going to extra steps to secure it, because stuff slides all over the place. The bedliner beats up the paint...and they don't even look good, just cheap.
I chose rubber mat. Bedliner will wear your paint underneath after years of use and are slippery to items placed in the bed. Rubber mat can be removed easily for a wash, they have textured/rubber surface for friction, and a quick buff will remove any of the little "rubber bumpy marks" left on the paint underneath when removed.
PS: Experts may chime in with better knowledge, but I'd wait a period of time before I put anything over the new paint in the bed. How long? Maybe someone else has a good answer to that.
Edit: I just saw that @someotherguy and I said pretty much the same thing.
I had a rubber mat in mine for years but about 2 years ago had it sprayed. I like it so much better! Trash would get under the rubber mat and it was harder to sweep out the bed. After the mat gets a little age on it you end up with black marks on everything you put back there. My vote goes to the liner.