I don’t use the add-on from the add-on store. I also don’t host the Zigbee2MQTT instance on the same machine as Home Assistant, although I believe you can and still make this work if you do.
I have two device “servers”… A Raspberry Pi 3 hosting 2 instances of Z2M in docker containers, and a Libre Computer LePotato running the third Z2M instance plus ZwaveJS in containers. I use an external Mosquito MQTT server (you can use the one in the addon store), then one instance of the MQTT integration.
This keep all Zigbee devices under 1 integration event through they’re all spread across three instances of Z2M. Been running this way over a year now and it’s proven to be very reliable.