They were Industrial Metal indeed back at the old days. Now they're something like electro-something... They did just the opposite of what Ministry (as founders of Industrial Metal) did with their music.
Marilyn Manson definitely left their mark in Metal, they're regularly mentioned in documentaries about Metal, and I don't see any problem with calling em Metal. They're too much mainstream? Well every good and successful band eventually will break out from the underground, but I wouldn't call it being mainstream, just successful. They don't really appear in every TV show with screaming fans in the back etc.
