Yeh, although the Ent A had been retired at the end of the last film and while it made sense to open VII with the Ent B but you really needed the Ent A and Ent D onscreen together to make it a real event
Yeah, but we never see them go home.
So the E-A is taking one last trip around the block for old time's sake. Romulans start attacking both Fed and Klingon colonies/outposts, because Nanclus being unmasked just exposed their evil plans and they've got nothing to lose, so why not. One of the Klingon colonies attacked and the only ship in range is the E-A, naturally. It's already all beat to hell from the battle with Chang but Kirk does his Kirk magic and takes out 2 of the 3 Romulans before the E-A eats it. The Klingons see Kirk and crew and the Starfleet flagship die to save their colony.
Skip to TNG, and they can still do Worf's promotion ceremony and have the bit with Data's emotion chip and whatever about Picard's family dying in the fire. Then the time hole opens, the E-A comes through and you do the Wayne's World bloobity-boop and things change.
Then you go from there. Our heroes figure out the reason they're at war with the Klingons is because in their timeline the E-A fled the battle instead of sacrificing itself to save the colony in a final gesture that would have truly united the two peoples. You have to have cool/fun moments as the two casts meet and share moments together. blah blah blah. At the end, Kirk goes rogue and takes the E-A and goes back through the time hole and sacrifices himself to save the Klingon colony. All the E-A crew remains aboard the E-D as the timeline changes.
The E-D crew doesn't understand/doesn't remember what happened but the E-A crew does because to them it's all part of the same timeline - they didn't jump from one branch to another, they came up to the "alternate" branch through the trunk. If that makes sense. And they figure out a way to exist in the timeline alongside their potential other "future" selves or whatever just like Prime Spock did in the Kelvin timeline.
I don't buy the "alternate characters" hangup because the characters in the Yesterday's Enterprise split timeline were not very different at all. It wasn't like they were awful mirror universe parodies, they were the same characters basically.
The only thing I can't really figure out is what to do with Worf in the war timeline, although I think even his total unexplained absence would have poignancy by him having his whole big promotion scene and then reappearing at the end, which reinforces the notion they're back where they came from.