When you say the Port is setup to deliver to two zones, do you mean you group the Port to either the stereo setup or the Surround setup, and the port itself is not connected to any amplifier?
Looks from your spec like the phono preamp supports both Moving Magnet and Moving Coil, so I don’t see you should have any issues even if you change cartridge type.
The analog connections from your turntable are pretty far removed from any of your Sonos speakers so I’d say there is nothing you can do on the phono pre-amp that can cause any damage to them. The worst you could do is cause damage to the Port, but even that’s tough as the signals from a pre-amp are not in the high voltage category so I really would not worry there.
Selecting MC for a MM cartridge might produce a distorted signal as the pre-amp will try and over amplify the signal, but unless you have the Sonos speakers set really loud, I doubt the clipped signal will matter as I’m sure you’d recognise quite quickly!
You are correct I group the two zones, and also combine them to “play everywhere” quite a bit. There are times where if volume on the preamp is too high and I raise the volume on the stereo pair two high its an issue. So what you said makes sense. I find it varies from one record to another. In some cases the volume is too low on the amp for a record, and I increase the volume. And when I play another record in that same setting its too high. Can I assume this is just a reflection of the quality of the vinyl recording?