A bit more playing around led me to a (if not THE) solution. I found an "enable headset buttons" check box in Meridian, which prompted me to dig further into BeyondPod, where a found a similar setting.
Everything works as I'd like now.
I've since gone back and checked a couple of things though, which are not quite as I expected. I thought if you re-enabled the controls within one app, it might disable the other. This isn't quite what happened. When I re-enabled Meridian, it responded to the controls, although BeyondPod still showed it as supposedly responding, which it didn't. Once I'd disabled Meridian again, I had to go back into BeyondPod, disable and re-enable it's control in order to have it respond again.
My main gripe was that if I were listening a podcast, and bumped the headphone controls, the music would start playing over the top of my podcast audio. While it may be a cute multi-tasking demo, it's not a particularly practical use of this feature, IMH(BC)O.