I would really like to be able to have both versions installed and working with remote buddy if possible. Plex/Ht seems to be able to do some things that I can't do on Plex, but equally Plex/HT can be a bit unstable so often still use Plex. 

Remote Buddy will control the latest generation of Plex that it finds while Remote Buddy launches.

For added clarity, here are a few scenarios:

1) If you have Plex and Plex/HT installed, it will control Plex/HT. 
2) If you have Plex installed, it will control Plex. 
3) If you have Plex installed, launch Remote Buddy and then install Plex/HT, Remote Buddy will control Plex. You need to relaunch Remote Buddy to control Plex/HT. 
4) If you have Plex/HT installed, launch Remote Buddy and then install Plex, Remote Buddy will control Plex/HT. You'd need to remove Plex and relaunch Remote Buddy to control Plex/HT.

Supporting both Plex and Plex/HT could create problems as 
1) most users just upgrade to the latest version and want to keep their mapping. It’s impossible to control two different applications with one Behaviour, though, especially if they run concurrently: 
a) if an action gets triggered, to which application should it be sent? Plex or Plex/HT? 
b) if you select Plex from Remote Buddy’s menu, which application should be launched? Plex or Plex/HT? 
c) if you want to forward Apple Remote button presses via Remote Buddy’s Virtual Remote, it can either end up at Plex’ helper tool or Plex HT’s helper tool. Running two helper tools both targeting the Apple Remote but routing events to different applications is a recipe for problems best summarized as the typical „the Apple Remote does not seem to work“ scenario.

2) implementing different Behaviours for Plex and Plex/HT would mean that you users would need to manually make any changes they made to their mapping settings for Plex after the upgrade. This is undesirable as it would affect the majority of users.

It would be great if there was an easy solution to this problem, but unfortunately there isn’t, so the only thing I can do is choose the solution that creates the minimum amount of problems for the minimum amount of users.

If Plex didn’t ship two different versions with different helper tools, different bundle identifiers and different UDP ports - none of which offers a direct, compelling benefit to users - these problems wouldn’t exist. Likewise, if users would experience Plex/HT as more stable, even fewer people would wish to use both versions. Unfortunately, I can not act on either - I can only react and try to make the best of the situation.

Best regards, 
Felix Schwarz 

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.