I doubt you can make a mod for another game with 3DGS.
That's just about the only limitation I've ever thought of (and I didn't even think of it)
All 3DGS does is put 3D models and pictures on the screen where you program it to, and update where they are every frame. That's what every game engine does, so you can make any game with it.
HOWEVER -- a "real" game may be more optimized for specific feats and will probably run faster given the same code logic. Also, currently 3DGS uses DirectX7 which doesn't have all the special effects of DirectX8 (most people's PCs only use DX7 anyway, regardless of if DX8 is "installed").
Also, a storebought game has a studio of people working full time, educated and experienced in their specific tasks. It would take a single person* a year to create what a studio can make in a week. If you're serious about making a professional looking game on your own and have any sort of deadline, you'll probably have to buy your models and textures.
*assuming that person doesn't have 5 degrees in assorted fields.
3DGS is a great introduction into 3D game design, and a useful tool for a studio, but in effect only eliminates one (the most elite) team, the engine programmers. As far as I'm concerned, 3DGS is the best of the "game development" products. The language is slick once you learn it, and the results are very good.