Yeah I understand that you say so but that zigpy message you are getting seems to indicate otherwise. So are you really 100% that you do not have the ZHA integration installed and it is trying to connect to your Zigbee Coordinator? If you do have the Zigbee Home Automation integration installed but not using it then you should disable or remove or at least make sure it is not trying to connect to your Zigbee Coordinator (which the zigpy mesaage suggests it is doing).
I might be wrong (as I am not using the multi-protocol addon or multi-pan firmware) but far as I known ”zigpy” is a library that is only used by the ZHA (Zigbee Home Automation) as a dependency. At least to me a message that mention ”zigpy” suggest that you have ZHA installed.
Regardless, you should flash the SkyConnect with EmberZNet NCP firmware and disable the multiprotocol addon then reconfigure for that as Zigbee2MQTT does not officially support it (and it is experimental anyway so not even recommended for ZHA). That information is available in SkyConnect docs as well as mentioned in Zigbee2MQTT docs too. See
And