I still don't really understand your issue; the scripts I used can easily be modified to be used regardless of whether any application is active or not. You could even choose to create a Plex on/off toggle script using if-then-else logic and put this under one of your remote buttons, and make a similar one for EyeTV. In those you can still insert logic concerning other applications (like close EyeTV live window if you activate Plex etc).

What you seem to search is to expand the basic "activate" function with some extra logic. Felix may enlighten us here, but in my understanding the action "activate" is a basic Apple function just like "quit application" is. Remote Buddy has these basic behaviours standard in the menu of every application you enable through Remote Buddy. I don't think it is possible to remove these basic functions from the menu. You can only add your own scripted actions. But if you do no use the on-screen menu of Remote Buddy but only the buttons on your remote for direct actions, I don't see why this 'hack' as you call it does not do exactly what you want.

It seems to me that the workflow you seek can be easily realized by some scripting...