[Suicide Junkie]

There is a VERY large distiction between having multiple mods installed and running multiple mods at once.

You don't need anything to have multiple mods installed for SE4. And any program to merge arbitrary mods in a logical way would be insanely complex, and there is no guarantee a logical merge will result in a playable mod.
Many mods are inherently incompatible because of their basic ideas.

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1) NEVER overwrite your stock datafiles.
2) Put modfiles in mod folders
3) Use Path.txt (via notepad or modlaucher) to switch between them.