Let me put this in simpler terms for the layman.
You had mentioned loading two scripts. Now you also had said what if the scripts use the same variable and prefix (e.g. %mp3.sayinchan was ur example) Now, what is the harm in having the preferences carry over for both scripts. If you don't want an mp3 advertisement in one, why would you want it in the other. In fact, that more a benefit than a discouragement.
I also explained why would you have two scripts loaded with the same purpose. Say you did have two loaded, would you have both in operation at the same time?
My point is, if you don't want the problem to occur, make the identifiers as unique as possible. My mp3 player uses an Ini so such things don't happen, but I could just as well used ktmp3 for KingTomato mp3, and avoided the problem right from the start.
My example was something like %mp3.dir (the assumed directory your music is located) Why would you want to have a different value for both players? Same with most other variables. If they have the same name, chances are they have the same purpose.
