Erhm, this is not an expert advice... I just have a limited knowledge of this. So take it as that. And I am sure there's better ways...
Well, there's a few different options you have, you can take the badold one, and separate all the custom content dependent parts to their own components in the mod. Or use a system that just checks if the mods are installed somehow and then install the additions if they are, in the same component as the original content, or in one component made to be installed later in the install order(aka cross mod content component).
I say somehow cause there's various ways.
Some mods have marker files, the BG2Tweakspacks mod for example has a marker files called cdt<number>.g3 and they can be checked by IF_FILE_EXISTS_IN_GAME cdt<number>.g3 ... aka
IF_FILE_EXISTS_IN_GAME cdt00010.g3 //the Remove Helmet Animations component is installed
//insert code
END
Other ways include checks if the mod is installed to the game, this can check if the G3Fixpack primary component (0) is installed to the game.
ACTION_IF MOD_IS_INSTALLED "setup-bg2fixpack.tp2" "0" BEGIN
//insert code
END
It should(never used this myself) check if the weidu.log contains the component. And if it doesn't, it just doesn't run the //insert code -content. And both of those codes can be used inside the main component, as an independent argument. And with a small tweak, they can allow the side component to install.
Yep, Jarno Mikkola. my Mega Mod FAQ. Use of the BWS, and how to use it(scroll down that post a bit).
OK, desert dweller, welcome to the sanity, you are free to search for the limit, it's out there, we drew it in the sand. Ouh, actually it was still snow then.. but anyways.