It's just what I've been taught by those that went before me and I've grown to respect it, it has become my comfort zone. When i got back into writing I asked for advice from a few people and basically got the same answer, "Protect your work before passing it around". Fortunately I've never been given cause to distrust anyone I've dealt with, including original works.
Yes. A way of protecting your work is registering it. But, the act of registering it does not grant copyright. You had that at the moment of creation.
It's not theft of work that is the biggest problem: it's contracts one signs when they are selling it or licensing it. That's when you should get someone who really knows contracts. Not a friend who says they know. But either a guild or a lawyer.
It is possible that some owners of intellectual property could encourage derivative work and grant copyright assignment.
It's possible. Sure. But generally MONEY is exchanged. As you you are giving the owner some money so you can do it.
Someone else might know if the Star Trek franchise ever withdrew the right of assignment in the past, I don't know their full history. From my non professional research you have copyright assignment until it is withdrawn.
I'm going out on a limb and bet: CBS/Paramount has never granted copyright to anyone regarding Star Trek. Looking now at "How Much For Just the Planet?" by John Ford, the copyright is assigned to Paramount Pictures. Paramount sold Pocket Books a license to make Star Trek novels. I suspect the writers of said novels were under Writers For Hire, so, they don't own anything they create.
The owners of Star Trek could pull their license, like they did with FASA.
So, the reason you aren't finding someone's copyright assignment being pulled, it's because you aren't finding a time CBS/Paramount GAVE someone a copyright.
Once the guidelines came out, rule # 9 concerned me greatly it is not a "Guideline" because an IP holder can either grant copyright assignment or they don't. If they expressly forbid assignment there is no copyright and hence no ownership to your derivative work.
I don't think you can own derivative period, regardless of Rule #9.
Warner Brothers haven't put out any guidelines regarding Harry Potter, that doesn't mean I can write a Harry Potter novel and own the stuff I create. It's all from a poisoned tree. Even if I COULD copyright my Harry Potter novel, I can't sell it, I can't publish it, I might get the shit sued out of me. The most I can really do is give it so some friends to read.
Why are you so concerned about protecting work that isn't yours? By that I mean: why are you so worried about copyright on a Star Trek script? Are you worried another fan film might "steal" it? I don't think a copyright on derivative work that isn't yours is going to offer protection anyway--that would be one for a lawyer with more familiarity of copyright.
Perhaps you could consider the framers of the guidelines didn't even consider the ramifications this would have on script writers, perhaps it was meant for something else. Maybe I have it all wrong but that's what it says and it exceeds my knowledge at that point.
I'm sorry to be blunt: but I'm not sure what the ramifications actually are and how they are a problem.