real mods don't go in your base folder
they go in their own folder under GameData. Not many people know that and I just simply think it would be easier for people as well as present a larger level of professionalism. You know.. to show that you took the time to present your mod well and so more and more people will want to play it.
Plus if it's a TC mod like I noted that I was requesting people do this for. You also have to include the modified source code and while yes this is done in the pk3 as well, it all goes back to visual aesthetics and making your mod presentable.