Actually, it's the same with macOS integration : Thunderbird do not take account of the Internet Account that are setup in macOS Settings.So if that's done, please do it for macOS too
I'm a heavy user of email alias set as account identities in Thunderbird, to get more control & privacy.I would be very happy that Relay is integrated to be able to automate and manage Sender account identity=Relay alias and encryption, on the fly or...