The Saturn manuals detail how to do direct access to the controllers from the SH2, but I don't see why you'd want to waste valuable cpu time if you have a coprocessor that can handle them for you. So it's easy to see why Sega didn't want people directly accessing the controllers.
![Laughing :lol:](./images/smilies/icon_lol.gif)
But there's nothing to prevent you from directly accessing them in your own homebrew.
As to the controller support line in the rom header, how about putting "rings" around the Saturn values?
MJ6<MKJ8>
Anything inside <> would be interpreted as Saturn, so you could reuse letters.