This is definitely a miss understanding. The new universe that has no relation with Prime Universe doesn't mean that it's not Star Trek. I can give you an example, by using a Japanese Anime Franchise. Gundam. There are a lot of Gundam series. A lot of them has the setting that different from the original Gundam world setting / universe. The story is different, the technology is also has different taste. But they still Gundam, because they still has similarity with the original Gundam World, although at the same time different.
The universe is new, clean. But you still can put the similar races like Vulcan, Klingon etc with new aesthetic, behavior, history, etc. The ship can be the same USS Enterprise, with similarity basic model, but give the artist a great deal of freedom to make it better. The tech can be similar or different, depend on the time when this series is made.
JJ-Abram is also happen in a new universe, but they still have a relation with Prime Universe, and not only that, they break the Prime Universe by destroying the Romulus. So why not just make another new Star Trek universe that won't disturb the two existing universe so the studio can expand the creativity without afraid of the past continuity?
Prime Universe = complete
JJ-Abram = Paramount Picture for Movie
new Universe = new series