About Gwen 10. Recalling for memory since it has being 10+ years since I watched it:
That episode is bizarre. There is an omnipotent narrator that can alter reality and decides it is going to show us, the audience (breaking the fourth wall) what would had happened if Gwen did get the omnitrix. Until that point everything is OK. But... it turns out that the Ben from this universe is OUR Ben, he remembers being in the middle of summer, not in the first day, and is as confused as us. So somehow the narrator broke the series and magically transported Ben to the first day of summer, with intact memories. And then since Gwen is better with the omnitrix that Ben, Vilgax sets his season 1 finale into motion earlier in the same day (I don't really remember if it was the same day, but if not, the next day). How? Wasn't he waiting because he was healing himself? Has he healed faster because of the motivation of defeating Gwen or what? And at the end of the episode Ben recalls that he had the omnitrix briefly removed from him in the season 1 finale and rushes to grab it before Gwen, but the last twist of the episode is that... Granpa Max grabbed it before and now he is Max 10. The next episode the omnitrix is not on Max or Gwen and Ben is again in the middle of summer vacation, without memory of that episode having happened.
Yeah, I know, alternate universes, but this episode Ben was clearly Prime Ben up until that point and ends in this new altered timeline with no returning.
Also when a Gwen 10 appears in Omniverse I just get the impresion that she is just supposed to be just "Gwen from an universe were she grabbed the omnitrix", simple as that, not "Gwen from a universe were Ben grabbed the omnitrix, have adventures with it, a fourth-wall breaking narrator transported him to the first day of summer, Gwen grabbed the omnitrix, then Max grabbed it and Gwen got it back again at a later point"
I don't know if you understand what I am referring about that episode. I feels so as a different thing from an alternate universe.
I haven't seen "Goodbye and Good Riddance" (In fact looking at the episode list, I think it is in fact the only episode of original series Ben 10 that I missed as a kid), so I don't know if the narrator gets into the plot or if in this case just presents the events and lets them unfold without intervention.