TTN stack V2 does not implement the new Basic Station protocol. Somewhere in between your gateway and the TTN stack there is a process running to translate the new protocol back to the ‘old’ Semtech UDP protocol. The sources of the Basic Station packet forwarder include python code for this purpose and a quick glance does not reveal any code handling the channel.
The channel number is based on the configuration. The frequencies defined in the configuration block is matched. So any gateway using a configuration with frequencies defined in a different order will report a different channel.