That would work if there was a change to mod.ini files.
Right now, let's say mod A has "mod B" in it's mod.ini, and mod B has "mod C" in it's mod.ini. When you load mod A directly, it'd load mod A and mod B, but not mod C. If you load mod B, it'll load mod B and mod C.
Now, if there was a way to tell the launcher, when you select mod A, to also select mod B and mod C, your idea could work. I'd see it as a mod.ini parameter, like +load other mod ini files line. If the launcher detected it in mod.ini of a mod you selected, it'd check for mod.ini files in all mods it references, and if they're found, load additional mods they reference. With a few checks to prevent loops, this could actually be a very useful feature.