Oh no worries, I enjoy people taking the time to think these through. I think I've discussed theming for 3 a bit in the dev logs though, definitely recommend reading those if you haven't.
As for the endings, not sure what you mean by significant. The credits indicate a "full" or "real" end, ie that you've gone all the way through the story for the episode and concluded it one way or another. Lack of credits is meant to imply that things got cut short part of the way through, and there's a lot more to see. My memory's a little blurry: did I do credits after the normal loss? If so I guess credits don't indicate a scenario that could carry over to the next game, but title drop then credits probably do. I think that was the intention.
And yes, as discussed, various things that happen in GT have the potential to be reflected in 3, just like stuff from 1 was reflected in gt.