I have to archive large accounts for past employees. My current workaround is to download all mail and labels using Google Takeout, then use Apple Mail's import feature importing them as Apple Mailboxes (not mbox). This produces the correct numbers in GEU. But boy... that's some waiting around for these large inboxes.
My observations in the V2 folder helped me learn that Apple Mail doesn't keep multiple copies of mail data where it would exist in two places. Instead, it seems to maintain all data in the All Mail box and reference the message copy in it's other folders. Makes sense with Gmail but that's probably why GEU isn't seeing mail in subfolders.
Any help?