Bose uses there own DSP settings strictly for Bose Speakers on all amps that I've encountered.

I once had an existing install that i had to service with a TOA Mixer/Amplifier, Bose Amp (not sure of model) and Bose Lifestyle in-ceiling speakers.

Sound was OK at best with the existing setup. Tried removing the Bose Amp from the mix and sound was even worse. Also tried several attempts adjusting the TOA to make them sound better. Nearly impossible, spent too much time on it and decided to just leave it in place. Luckily, they were using the TOA for input switching.

Maybe you could swap the amps out for newer versions, maintaining the specific DSP for the speakers but also adding the aux inputs for every zone. I'm pretty sure the newer amps have an auto-sense trigger to turn on the amps. Or at the very least, leave amps on all the time and just use the Sonos connect for music selection and volume control.