Okay, fair enough. Personally wouldn't consider that a retcon, since it's possible the future and one alternate universe are essentially the same. I think Paradox said alternate universes aren't in sync so one time could have reached the Ben 10,000 period earlier.
"Time is set in stone" is only one of many time travel theories, none of which are proven and all are equally plausible at this point. One theory states if you go back in time, you've already been back and the changes you made are already felt today (basis of the Bootstrap Paradox). Another states time is in flux and can continuously be changed, which is what Back to the Future went with. There's also multiverse theory, stating if you make a change, it results in an alternate timeline forming in a parallel universe, while the present time remains untouched. And another main one is if you make a change that causes a paradox, it could mean the end of reality and all we know it.
I can answer that question with a trope; "Timey Wimey Ball". Named after a phrase originating from Doctor Who. It basically means, due to the countless time travel theories out there, sometimes shows will have a tendency to use one theory, but then later on contradict itself and go with another theory (sometimes within the same episode). Due to this overlapping of theories within the single work of fiction, there will be elements that seemingly make no sense. In addition, that whole Time Bomb was a lazy plot device, it did all that because it "needs" to, no science and logic behind why it does so. I think they explained it in-universe that it was meant to target the alternate Bens, and their timelines, but not something/someone from an alternate Ben's timeline in another timeline. I've gotten used to logic being ignored when it comes to time travel fiction. No point in hurting your brain trying to make sense of something that's not meant to make sense.
That I agree with. Focusing on 2 universes would be better. Although preferably the two universes had to have a significant amount of difference to make it interesting, like a mirror reality. If Ben just found himself almost exactly the same, that would be kind of boring.