For now I have created my own behaviour for Plex so that my remote works for both plex and plex/HT. It is not perfect, but it will do.

I understand what you mean about it being confusing for users and having there mappings move over to Plex/HT, so I can understand why that is the standard way for remote buddy to behave. However it would be great if there was a way of manually having both behaviours installed, with a few steps from you on how this can be achieved for those that wish to do so.