Alternate reality fails to make sense in this case.

 It has been done before in previous star treks. So this is both an alternate reality that is created by time travel. Yes I can accept this theory, however... This is countered by other star treks time traveling. Hell you might as well throw the premise around first contact out the door. The earth was turned into a borg capital planet before they went fully back in time. The Enterprise and Borg did not simply just go "missing." So now they just created another reality when they went back to future then? Or the countless other time travel stories in Star Trek. Let alone the Federation of the future monitors and polices time travel.. hummmmm....

Sorry not much of a trekky here. Just watched the shows and movies a lot. So my information could be flawed. It is just my opinion that this excuse is a cop-out not to bend the game to a new path. If STO does well, rest assured to see the other universe in an expansion. Especially if they make a 2nd "new" star trek. 

 Who can blame them with production costs of these games today.