Likely as not they were grandfathered in due to being in production prior to the guidelines being issued.Since then, I have seen several productions that basically violated the guidelines. A full feature (that needs a sound edit!) Also, a two part stand alone episode, that fully exceeds the 15 minute guidelines. As of typing this, they haven't been struck down by copywrite violations or cease and desist orders. Why is that?
This is far more my point of view. Honestly, if people make fan films it warms my heart even if it feels raw and amateurish. I mean, my college and high school years were filmed with amateur productions of SW, Matrix and Star Trek, among others. Some went better than others but we had fun with it anyway.Take the inspiration, and make something new. There's nothing wrong with a fan flick. I'm an easy pinch. I love them, warts and all. However, I'd be just as chuffed if someone would take all that enthusiasm and energy, and make something fresh and new. Just my thoughts on it. Your mileage may vary.
But, we also put in effort to make original content. And we had just as much fun. I would encourage people to take that enthusiasm for Star Trek and create something with that passion, either new or a fan film.