I had my amp put on the top of the box - no problems so far. I put it there as that is wasted space anyhow. I can fit a jogging stroller into my trunk still even with a 12" sub. I can't believe anything would hurt the electronics - that's just not realistic.
The rear deck gets pretty hot I've noticed, so I would not put it there. My amp gets hot (when not being used) on sunny days from heat from the deck. My amp is 6-12" below the deck, but the infrared or plain old heat gets to the amp. It seems fine though, and friends have since told me they'd had amps mounted below the deck just fine.
