or spike on the AUDIO CABLES, but not the amp remote line. The amp remote line is there to PREVENT pops.

That is correct, to prevent the "POP!!!" i.e. a DC voltage spike to your speakers the amp(s) need to shut off just before your head-unit does, which is why the remote line powers down first (or at least it should) just as the head-unit powers down.

And there should be a way, if the hardware has a watchdog support, to preform a set of instructions if the software is locked up and if so is that something the Empeg/Rio team needs to set it up or is it something we can add, I say hardware only because I build servers and they have the watchdog built-in but it usually just writes a log file if the system locks)