I assume you meant the amp under the TP was relocated to a saddlebag. I've heard of a few people doing that when they converted the TP to a quick release setup, but never heard one way or the other about the heat factor. Those amps aren't exactly compact, and they were meant to be mounted where air can flow around them. I would think cramming one in a saddlebag with no air flow would be a good way to shorten the life of the amp, even if it didn't melt anything. If you further confine the amp by adding a liner or "luggage", I can't see where that would be a good thing. However, the best way to tell if you're going to have a problem is to mount one or more temperature probes and monitor the temps while running the amp hard with the bag sealed up. I'd check the temp of the actual amp and the temp of the interior of the bag and lid.
If it were me, I'd look at a better aftermarket amp mounted in the fairing and reclaim that lost space in the saddlebag.
JMHO - Jerry