Could Abrams and Lin supporting Axanar have an effect on the chances of them working with CBS and/or Paramount or at least in the Star Trek franchise again? I could definite see supporting the other side in a lawsuit pissing off the studios enough to not want to work with them again.
Hundreds of millions of dollars of profit are involved per film with these folk. I don't think anyone is going to tell them to go away.
OTOH, I don't think the studios will pass up a chance to erect a firewall against "independent, """"no profit"""" " productions using new media tools and distribution techniques.
I suspect the guidelines may, as others have suggested, be a preapproval case by case basis within a tight set of boundaries, to retain studio's right to use discretion rather than be forced into guidelines. I suspect Axanar's guidelines are going to be don't slam the door after you shut off the lights, and take your stuff cause it won't be there tomorrow.