Currently, the --drive-service-account-file flag is great because you can specify a JSON file location and use it to copy to your TeamDrive, thus, in theory, eliminating the 750GB daily limit per account. The issue lies with that it cannot read from the My Drive. Hence causing permissions issues where it can't see My Drive when copying between "My Drive" and "Team Drive".
It would be great if the MAIN account owner of My Drive could be set so that, when using the flag --drive-service-account-file flag it can read the "My Drive" mount without any issues.
Edit: I do realize that you can share a My Drive folder via email to the service account and use the --drive-shared-with-me. This works fine when you share an individual service account email, but if you share it with a group email that contains a bunch of SA emails then that does not seem to work.