Food for thought...
Your system will accentuate any loose panels and rattles in your vehicle. It will vibrate your amp no matter where you mount it. What it the most solid part of your car with your system installed? If it is well built, probably your sub enclosure. If your enclosure is vibrating a lot then you are losing a lot of bass energy and the enclosure is heavily coloring the sound of your subs. Also consider that unless you are working with a luxury car that has a really smooth engine that is well damped and well isolated from the chassis and has a very plush suspension, the car will provide more vibration than the system. Add any kind of stiff performance suspension and/or stiffer motor mounts, and you compound this greatly. Any component made for the car environment is made to handle vibration. A well built amplifier will not have any components vibrating loose inside of it. If it does then it is not well made. I would spend my time and effort making sure that everything is well mounted rather that worrying that there might be a tiny bit of vibration added by mounting to the sub enclosure. Your sub enclosure should not be just sitting in the trunk or hatch anyway. It should be secured somehow for safety reasons. One easy way to do this is with plumbers strap. Screw one end into the box and sandwich the other end under the seatbelt bolts. Now if you have to make a sudden stop or someone rearends you or you get into some other type of accident, you don't have a large projectile moving around in the back of the car. This is especially important in hatchbacks and SUV's where there is no trunk to protect you. Also think about what would happen if one of your power wires comes loose in an accident or from stuff shifting in the trunk. You will have a pretty nice spark show before the fuse blows that could cause a fire. That is what I would be worried about, not a little bit of vibration that the amps were designed to handle anyway.
