Someone else had a problem trying to access Joplin server from a sub-directory off the domain rather than using a sub-domain. In that case the reverse proxy was nginx.
What appeared to be happening was that the user wanted to access Joplin from /joplinServer under their domain. The proxy was adding /joplinServer to the base url value which itself already contained /joplinServer, so whilst the actual path wanted was https://domain.com/joplinServer/login the proxy / base url combination interpreted it as https://domain.com/joplinServer/joplinServer/login, hence lots of 404s. The joplinServer could not be removed from the base url as then the base url did not match.
I managed to sort it for nginx by telling nginx to ignore one of the joplinServers using a rewrite. I mention this as it could be that the same is happening with HAProxy so it is something you could investigate.
The easiest solution is to access Joplin Server from the sub-domain https://notes.example.net but I guess there's a reason you do not want to do that.