I have noticed that the default URL regexp redirect for servers when created is being set as /(?!.well-known)(.)$. Shouldn’t this be ^/(?!.well-known)(.)$?
Not sure if it makes a difference but when I leave it as the default (without the initial ^) Let’s Encrypt fails. Only just figured out what I think is causing my failures but now I’m blocked for an hour so can’t see if this has resolved the issue or not.