What dude with the Blazer and L7's said is accurate in my opinion. I have had my RF T4k mounted on my box for 11 months to be exact powering 2 BTL 18's and have ZERO problems. I think what to be considered are these things:
1) Is it a quality made amp? Around the lines of say Fosgate and the like compared to something like Sony etc. Reason being is quality behind the manufacturing and production of the Amplifier and how the internals are soldered, bolted and placed. Obviously if the amp is of lower quality one would assume that the time taken to solder, bolt etc is not as great as in a higher quality amp thus vibration = rape at a higher rate if lower quality.
2) Is the Box made properly? If the box is properly made and reinforced your box SHOULD have ZERO flex in which case it doesn't matter if your Amplifier is on the box, on your back seat or on the floor. In my opinion on the box would be the BEST situation if it is mounted properly. Reason being if you think about it your box should either A) Be bolted or secured down to prohibit movement or It weighs a shit ton so the likelyhood of it getting movement is low. Think about how many people have their amp mounted to back seats(Meade), floors(Meade) etc. This to me would vibrate MORE than on a box that has no flex. Perfect example that everyone would associate with is Meade's truck... The mofo has them mounted in every form possible other than on the damned roof... He has them on his back seats, on his box AND on the floor under his box... Does he have problems with 30k?
All in all I am a Best Buy Autotech and mount Amps on prefab boxes all the time if spaces requires or customer requests. I also mount them on the back seats or floor usually for a nice clean look and to eliminate the risk of the box+amp bouncing around and pulling a ground or damaging wiring. In my experience I do NOT have any more problems with customers returning with amp issues on one or the other. If anything its on Amps mounted on the backs of seats in a trunk because people are smart enough not to put anything near the sub but LOVE to pile up laundry, dog beds, supplies and random other bullshit right ontop of the amp and of course the bastards gonna get hot....
In closing: BUY GEWD AMP, BUILD GEWD BAWX, SCREW IN WITH BIIIIIIG SCREW MAKE SURE NO SHAKEY SHAKEY
Fin