Looks like if you ignore parts of the wiring instructions it'll work "as expected" ie not turn off the slave HU. I'd be very surprised if the switch would have a problem with there being signals coming in on both sets of RCAs simultaneously.

I'd hook up the amp remote outputs to the switch as described (and RCAs), but not use any wires from the switch to power/turn on any of the HUs. Instead split the existing (or run new) power / accessory wires and connect the HUs to those.

Also, doesn't look like there's a useable wire from the switch to run to the amps remote turn on. Easily resolved with 2 1N400x diodes to tie the 2 remote turn on wires together into a single wire to use to turn on amps or power a relay (to create a more powerful remote turn on).

/Michael