Let me say something stupid here...
How do you think amps are designed to be run? I mean, theres a reason why the mounting tabs and screw holes are on ONE side, because THAT side is the side it should be mounted on. Be it your trunk bottom, back seat, your roof, your box, or hell your ass -- thats what its made for -- doesnt matter where its mounted.
And as far as an amp getting "hot" or not -- it all depends on the amp. An Audiobahn amp -- yes, most likely will get hot, RF, yes... most others? probably not -- less its like a 2000 watt monstor amp, but hell it gets hot anyways so it shouldnt be too much of a problem
But like the others said, mount it, run it for awhile... see if its cutting out -- if not, bingo there you go!