I use my EISY for Insteon devices and scenes.

I'm looking to add automated window shades to my house and need to choose the type of motor (Zigbee, ZWave, Matter over Thread).

I'm leaning toward Matter over Thread for the shades. I don't have Zigbee, ZWave or Matter/Thread in the house right now.

I'd like to control these from my EISY rather than adding HA to the mix (probably through a bhyve VM).

Would an Aqara Hub M3 theoretically work with the EISY Matter Beta support? Since it would plug into my network, the EISY would need to find it that way. Of course I can fix the IP address and specify if needed.

If it's Matter over Thread, you'll need a border router. If the Aqara Hub is also a border router, it should do. You don't need the ZMatter dongle. You'll need to configure the device on the Aqara hub first, then share it to the eisy. There's also the question of whether the device itself will work with the eisy (Matter is still in alpha testing). If it's basically an on/off device, chances are good that it will work.