If you do not allow a mod - any mod - to overwrite files, it will not function as it's developer intended. Either trust the mods you install and let them overwrite, or don't bother with them.
It is possible to tweak mods and merge files so that inherently incompatible mods will work together. But that requires some knowledge of modding and the mechanics of the mods you try to merge. If in doubt, don't activate it.
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