Sorry to hear its not working for you. It was tested with MV/MZ images to push to the MZ program. Probably the image folders are in different locations/names between MV/MZ.
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They absolutely aren't. I own both programs so that's an easy check to make, they DO differ in their gradient files though. Otherwise I'm not sure why MV's base stuff at least completely bricks the generator. Otherwise your tool works if you manually add subfolders that do not exist in literally any asset pack you can buy. Something you should probably add to how to use the tool on that note. But yeah folders are identical and such, but those extra subfolders are not there for effectively ALL paid generator packs, like I mention in the earlier comment the Japanese asset sets are the only ones that do include them.