As I understand it no, the modloaders will still handle things like file management and conflicts. Individual mods could implement solutions for that, but it makes more sense to centralize that effort around the modloaders.

What this will do is make it much less tedious to develop the mods in the first place.

(I may be wrong and the role of modloaders may have changed in the six years since I was last active in the modding scene without my knowing it)