I had just fixed this problem in El Cap when I updated to Sierra, and it came back in full force. The solution is simple though. In this version of the Mail app there's no more checkbox for saving drafts on the server, but you can manually select where Mail stores your drafts for you.
As before, go to Settings > Mailbox settings and in the Drafts drop-down menu select either [Gmail]/Drafts or [On my mac]/Drafts.
Selecting the latter option will prevent Mail from sending your drafts to the Gmail server, resolving the problem with leftover drafts.
Obviously, this does mean that you can't work on your Mail drafts in the Gmail web version.
