Hey, Aureliano! Long time no speak! (Like, since the early 2000s).
My best guess on the trademark issue is that the most apparent trademark Axanar would be using is "Star Trek", and I remember reading about a year or so ago that, at CBS' request/demand, Axanar dropped all uses of the phrase "Star Trek" from their title and other marketing, which is why it is now simply titled "Axanar". Sure, that doesn't mean that a claim still couldn't be brought on the prior use up to the applicable statute of limitations, but it wouldn't really support one of the things that the current complaint seems to ask for, which is an injunction against an ongoing or imminent infringement. That's my best guess.
Of course, there are still other potential trademark claims arising out of the overall similarity of ship designs etc. on a theory of "trade dress " but there are hoops to be jumped through there because the trade dress is most likely not registered – plaintiff would need to prove not only likelihood of confusion but also that the trade dress had acquired "secondary meaning" (i.e., that when someone looked at this designs they immediately associated them with Star Trek and not just some generic sci-if). Seems like that wouldn't be much of an obstacle but I guess the studio thought, with the low – hanging fruit of the copyright claim, why waste the time and put themselves to the extra burden of additional claims?
M