Yeah that does seem like it would be amazingly difficult (if not impossible) to do from a script.
Assuming the way that Plus! modifies them is by using detours to proxy resource loading functions (LoadResource etc.), then a script would need to also do this, correct? I'm guessing it also would depend on the order in which things are loaded. If WLM has already loaded uifiles before Plus! has initialised scripts then our poor scripts don't stand a chance of doing this
It's also important to note this isn't something which can really be done "on-the-fly". You have to restart messenger for any of the uifiles to be reloaded. It really does seem messy to be modifying Messenger like this from a script...
Would it be easier to create custom buttons using a skin with certain cmdids that you could then process by subclassing the window?