I added mod support in my own themes as well, however I did not use a user editable setting, because most of the time users can hardly even find their way to the current theme settings (even though in my themes I added a button in the header to directly go to that page), but most importantly if the user enables support for a mod using that setting and the mod is actually not installed, that can lead to him getting locked out of the forum because of an internal server error where the theme calls for a mod function that actually doesn't exist in the code base.
If you want to add support for other mods, I would highly suggest you try what I did, for example vbgamer45's Like posts mod has a "LikePosts" php class, so what I did was test if the class exists or not to tell if the mod is installed using the class_exists() php function, the same can be done to mods adding new functions, you can use function_exists() but only if you're certain that if the mod was installed that function/class would be accessible from the page you're testing it from. Also when using this method you should also make sure whatever function/class name you're using to test isn't used by some other mod.
It may be a little complicated but at least it's better than having a setting that may mess the forum up if enabled.
This is just my opinion, I'm not saying that it is not allowed as I haven't had the chance to hear the other's opinions about it.
