It essentially kills all fan films with high production values.
Of course. That's what copyright is for. If there is high-quality Star Trek
material available cheaply or free, especially if it does placement for rival manufacturers' merchandising, then Paramount won't be able to make [as much] money out of its expensive IP. The continued production of professional output in the market for Star Trek
material depends crucially on the IP owner's ability to keep the output in shot supply enough that people will still pay to see theirs, still buy official merchandise. If fans produce high-quality full-length Star Trek
material that will glut Paramount's market. They are being generous, perhaps calculatedly so, in allowing any rival output to be released at all.