The 2K epoxy based bedliners (out of a gun) will offer you a very tough coating that paint can't match...Properly prepped and sprayed, it's tough as nails. But like mentioned, don't plan on it coming out without a major fight. Also, I would want to put my eyes on the area to be sprayed before they apply it. Like Pete mentioned, good medium for covering shotty work. Another couple plus's with the bedliner is the resistance to environment, sound deadening and heat dissipation. I've seen the metalshield on a few hot rodder sites I visit, a bunch of guys out there are using it and actually contemplated using it myself. There are limitations to it's use and where so read up well. Back to the bedliner......My own opinion here, but I've seen too many Mopar trunks rotted out to just go with paint. Obviously old Mopars now days typically don't see the environment like back in the day, but never the less there's still driving in the rain, dealing with condensation and car wash's that moisten things up. If using a trunk mat...well that is like sticking a dagger in it....10-20 years from now I don't want to look at rot in my trunk. Fresh/clean metal coated with a couple coats of rust bullet, then bedliner should extend that timeframe long after I'm done walking the earth. If you're a car show kind of guy, I could see the bedliner not really being an option.
Do not use rubberized undercoating out of a can or roll/brush on bedliner for your trunk, floor or underneath. They're both more porous and applied wrong will actually hold moisture. The roll on bedliner is like cheap black paint mixed with shredded tires. Tried it, sucks! Not even comparable to the gun sprayed stuff. Honestly you would be better off with paint and a good epoxy primer underneath to protect your metal then those options. Also, I wouldn't spray the bedliner on just metal. Like I said before, a good couple coats of rust bullet (or similar) or over paint/primer will give you the proper base. Trunk spatter paint can be applied over the bedliner if you're looking to dress it up, but obviously still won't have the appeal of a nice painted surface. One more thing to mention, it will stink the car up for about a month while the catalysts are curing up. Bearable, but will be noticeable. Good luck what ever route you go.