I think absolutely this is likely how it's going to go. There were far too many hints of ZA stuff sprinkled throughout the game. I don't think you need me to repeat them at all, but just gonna put them down here anyway (with more i'm probably missing)
Hand holding through the Lifestream.
Zack looking up at the sky as reunion petals fly past as we cut to Aerith looking up at the same sky and asking Cloud what direction Midgar is at.
Multiple scenes at the end of seemingly Aerith helping Zack multiple times.
Zack ending up at the Church with blooming flowers saying worlds can reunite again.
Zack bonding with Elmyra and Aerith and Elmyra's house being referred to ingame as "Home" for Zack
These are just a couple scenes, but then even from the first scene of the game we see Zack's devotion to Aerith, and how he stays devoted to her throughout all of his segments, even if he is slightly upset and confused by what Marlene is saying, he doesn't hold anything against Cloud (obviously he doesn't know the full story or anything yet about what Aerith really feels or what Cloud feels etc) and see's the bigger picture is saving Aerith regardless. They can talk later.
Not only this but;
Aerith herself admits in Gongaga she still has feelings for Zack.
Reagrdless of what anybody thinks of what she feels for Cloud, there is no way you can deny she is confused and unsure about the Zack situation and and her feelings for him right up until the end of the game. (S5 date etc)
Cloud remembers his friend Zack this time around and how "head over heels" he was for Aerith
Aerith admits to Cloud that she likes him, but isn't even sure what kind of like that is, whether it's a friendly platonic like or a romantic
like (So for anybody to say she's currently head over heels in love with Cloud is wildly over the top)
Now I know in the English VA (Maybe not in the Japanese VA) they contextualise the Church as Cloud and Aerith's place, "our place" although I believe in the Japanese it's just "a place of memories" (I may be wrong on this). Regardless Cloud and Aerith have a whole one memory there, granted it was memorable but it wasn't like it lasted long either. Cloud seems to not even know where Aerith is talking about at first until she almost spells it out for him. However who do we cut too sat right outside the Church already? Zack.
I also don't think it's a coincidence they updated this keyart for Crisis Core Reunion
View attachment 15347View attachment 15348
Left is the original Crisis Core key art, and on the right is the same keyart but updated for Crisis Core Reunion, and it's putting them in the church.
Like at this point it would almost be completely negligent to the story if they didn't reunite in Part 3 considering all they've interwoven within it. If absolutely nothing else the reason why i go with your assumption that CT and ZA will be the endgame is because of everything that has happened in Remake and Rebirth so far it makes the most sense, to have CA be endgame at this point 2 games in would be far FAR too messy a proposition to realistically and properly pull off in Part 3 without pulling out massive threads of story and character development that has already happened. I feel like the time for CA to be considered endgame for P3 was to write the Retrilogy that way from the very beginning, or at least solidify it in Rebirth.
How are you going to explain Cloud remembering his best friend Zack and his feelings for Aerith, and then Cloud making the moves on Aerith not long after that.
How are you going to explain Cloud kissing Tifa and then immediately moving to Aerith and, say, kissing her or romancing her like nothing happened as if he's some playboy
How are you going to explain bringing Zack back and showing his total and utter devotion to Aerith in virtually every scene, only for him to get sent to the sidelines in Part 3, there's no way Aerith as a character would do that.
How do you explain making Tifa go through the absolute wringer for Cloud, physically and emotionally, only to say Cloud was just using her because he was jealous of Aerith and that's why he kissed her (a popular theory for some reason)
They could have easily created a CA love story without ever needing to do any of these things, or the other multitude of things they put in Remake or Rebirth, that would ultimately undermine the characters and the story. There's just so much more they'd need to either throw in the bin or somehow try and explain away like it never happened in Part 3. It would be absolute insanity to do this and I don't think a lot of people are fully coming to grips with this yet.
Everybody is free to ship whoever they want and honestly as long as it makes them happy that is what matters at the end of the day, but I think at this point things are only directing one way and i'd be mind blown if it didn't end up that way.