Sad but true: a big part of the hoop-jumping is a subtle test of how well the applicant follows instructions. It's certinaly not impossible to bend the rules, but simply sending something other than what they're asking for seems unwise.
I guess the underlying theory is, the ideal applicant would have a whole wide range of professors just dying to write letters on her behalf; if the school asks for letters from 2 science profs, a humanities prof, and a doc, then I would say the subtext is that (according to the school) you should be able to get them. If you send 1 science-prof letter and 2 humanities-prof letters, then at least be prepared to answer questions like "why couldn't you get 2 letters from science faculty?" or "what are your humanities profs covering up for you?"
See what I mean? It's probably not be the case that you couldn't get another science letter, or that you're buddies with the humanities profs and they're being intentionally rosy... but that could be how it looks. So wouldn't it be better to not open that can o' worms?