Well, it's not like alternate timelines are in any way unusual in Trek. As far as pop culture is concerned, Trek pretty much codified the "Mirror Universe" concept, and as of ST09, it's kind becoming our "thing."I think it's perfectly reasonable for us fans to treat them as though they constituted separate continuities, as, for our purposes, they might as well be different universes. But from a non-fan POV, they're no more separate "universes" than, say, the Batman comics and Christopher Nolan films are. They're just different versions of the story.
(And the DCU and Nolan films easily fit as part of the same multiverse; there are explicitly 52 different universes [and that would have to be just the DCU's "stream" --there are recorded "multiversal" crossovers with Marvel's 616-universe, which has its own plethora of alternate universes]. And this counts fundamental universe changes, not mere timelines [of which there would, of necessity, be billions more].)
I always thought the first Elite Force game actually made more sense than the show it was based on; Voyager in constant disrepair, sections of the ship blocked off, holodecks actually being used for training, personality clashes between trained Starfleet Academy graduates and slightly more eccentric Maquis, Tuvok and Seven putting together a dedicated Hazard Team (because they don't have the option of calling in Starfleet Marines).The closest videogame Trek came to fitting into the tv/film version was the old point-and-click games from the early 90's. Everything else includes way too much violence to really be a justifyable part of the tv/film/novel Trek universe - like Elite Force 2's massacre through Space Station K-7 (armed with a bazooka-style micro quantum torpedo launcher) in order to capture and interrogate a Ferengi.
Plus the DS9 game, The Fallen, which had the Dominion War and a Bajoran religious conflict as backdrops, allowing the violence to make sense. I actually find it more coherent than the Millennium Trilogy it purports to adapt.