Pretty sure that's not correct, Titi. Licensing is not per-mod. You can distribute packages that contain files with different licenses. Heck, MegaGlest does this. The engine is one license and the resources are another. You can do the same with techtrees, making one faction one license and another a different license.
Also of note is the concept of authors giving permission. For example, the creator of some mod package could ask Hagekura for permission to use parts of the mod where a licensing incompatibility may otherwise appear. It would only apply for the guy who asked permission. It's kind of a mess (since people wouldn't be able to derive from that mod package without also asking permission), but it's an option.
There's also the possibility of fair use. It's not really a clear cut topic, so it's not clear how much of a resource can be used under the concept of fair use. Better to avoid it.
Finally, there's a third possibility. Just use the content however you want. It's pretty much a given that the rights owner issues a cease and desist first (I suppose it's possible to open with a lawsuit, but I haven't heard of that happening and that's probably for a good reason). That means "take this down or I'll sue you". It's entirely possible that the content owner will let you continue, or you'll slip under their radar. There's a few mods for commercial games that are in a position where they could be taken down at any time with a C&D, yet haven't been. For example,
Pokemon Zeta/Omicron is a fan-made Pokemon game that obviously violates Nintendo's copyrights and trademarks, yet has avoided a C&D, somehow. Given its size and popularity at the time of its development, I would expect that Nintendo knows it exists, and merely chooses to let it exist.
That's not really in the spirit of development here, but it's an option. But it comes at the cost of having to either make changes or stop working entirely if a C&D is issued (I presume you wouldn't be in any position to challenge a C&D, unless you wanted to call a bluff).