I was just now able to manually add my broken custom domain/G-Suite address to Mail by doing the following:
1. Delete account from System Preferences -> Internet Accounts
2. Open Mail -> Preferences
3. Click "+" and choose the "Other Mail Account..." option
4. Follow the steps here to generate a Google App Password: https://support.google.com/accounts/answer/185833?hl=en
5. Enter in your email address and the new App Password
6. Voilà!
Jona, do you know if deleting the Gmail account from Internet Accounts will also delete the folders in Mail under "On My Mac"? I'm worried that deleting my Gmail account will cause me to lose those folders and the many emails in them.