Let me know what you hear back from virtualmin forums, as i was also debating bringing this to their attention.
My install is pretty much default in terms of front end web configuration. I have other websites on my box that were working correctly, but the one i was looking to fix didnt. Which is odd because they all run the same acme_tiny.py config.
I would seriously recommend not making any edits to files unless you understand why you are making them, its possible to make the problem worse.
In terms of the .well-known folder. No, you dont need to create it, the folder/file is generated at the point in time of the letsencrypt request within virtualmin SSL.
At this point i can only provide you with some of the knoweldge that was passed on to me. If i get some time i can attempt to look through the tools that i was given to troubleshoot me issue and i’ll see if i can diganose yours. But please dont wait for me.
Please keep this thread updated if you hear anything back from the virtualmin team.