From what I understand (I could not test that though, as there is no free version of the software), the generator comes with parts baked in that you are supposed to use to create the characters. You can then edit those created characters afterwards (with an image program). The other character asset packs do not seem to be expansions for the generator, but standalone graphics to be used and edited. You can basically see it this way: There were packs released to give you characters for your game making, and then at some point a generator was released to give you more freedom to create your own characters by building from the parts already provided in the software.

Now, depending on how open the software is, I can imagine that within its folders you may find the parts the software uses. So if you would use the same pattern for a part (for example the hair), you could potentially expand/replace a part-category with more (from for example the standalone asset packs), but that would take more effort to get working than if they would be actual expansion packs with the parts already ready to put in.

Edit: Keep in mind that this info is for the original version of the generator. The EX version seems not to be available yet (unless you got the bundle), so maybe that one has that additional feature.