MailMate looks into the default path from MacGPG to find gpg binary. The path is indeed different if you have gpg installed using homebrew or any other method. It is not possible to chnage the default path through user interface, but it is possible through hidden settings.
defaults write com.freron.MailMate environmentVariables -array '{ enabled = :true; name = "MM_GPG"; value = "/opt/homebrew/bin/gpg"; }'