Mod files should actually be going in MGS3/texures/flatlist/ovr_stm/_win instead, that way they don't overwrite the original game files, and you won't lose all your mods if you verify your steam files / whenever the game updates.
(ovr_stm is the steam / windows version texture overrides folder)
Had a question because keeping original files tidy is relevant to my interests: does that work if I as the user just download the mod and paste the mod files in the directory you specified? And does this method also work for MGS2?
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(ovr_stm is the steam / windows version texture overrides folder)