If the Bozeman
only underwent the events once, then from their POV, there should have been at least two starships E-D there simultaneously: one they collided with, and another they avoided. (Or would have, if not for having collided anyway!)
Clearly, the Bozeman
also experienced at least two distinct iterations of the events, one survivable, the other not. They may have been sucked into the future just once, but once there, they sometimes collided, sometimes avoided - for exactly as many times as the E-D did.
And the clock necessarily read the same every time, or the E-D would have noticed something amiss. One really wonders when and how our heroes managed to get out of the "time pocket" where the clock was stuck repeating the same couple of days (or, for the Bozeman
, the same couple of seconds).
Or perhaps we can argue that time didn't get stuck - our heroes simply did not enjoy constant access to this fancy "Federation timebase" and its informative beacons. Quite possibly, time was flowing normally everywhere outside the hulls of the E-D and the Bozeman
, and the phenomenon just created intact and time-retarded copies of each ship every time after the loss of both. But that would mean that the Typhon Expanse would stop spitting out new Bozemans
once the collision was avoided, which is a bit odd: why should the tiny collision dictate the behavior of the vast phenomenon?
The idea that time went looping within a specific volume of space is IMHO the most consistent one. Once the collision was avoided, our heroes could leave that volume of space (within which a looping phenomenon might still exist) and ask the nearest beacon what time it really was. They could have done that simply by not sailing to Typhon while within the loop, of course - but they second-guessed themselves out of that correct solution too many times in a row.