That's why I've always been against the authors giving the MC too much backstory. The player's choices should be more important than the MC's feelings, which are tied to events that happened before the game began. If the player wants to tell Zoey in Episode 9, "Let's leave the past behind and start over," they should have that option.
When I started playing, I quickly realized the main five weren't right for me, and without a second thought, I chose the "others" in Episode 8. It never occurred to me back then that the blue-haired former protagonist might interest me. I didn't even play the Interlude until Episode 9. But then, while playing Episode 9, I realized Zoey was the one for me. When I saw the "You can sleep in my room" option, I thought, "Great, now I'm going to fuck your gorgeous ass until the morning." But Zoey left for the train, and my balls were probably the same color as her hair at that moment. But the one that upset me the most was episode 10. The MC blurts out his confession and leaves because he has more important things to do, like talk to Nick, Jacob, and other characters I don't care about. I was furious. I didn't care about Maya's damn contract (The funniest thing is that they didn't need the MC's help. Maya and Derek just had to come home for the weekend, wait until Patrick fell asleep or went to the store, get the key from the garage and pick up the contract), all I could think about was Zoey running away in tears and there was nothing I could do about it. Now that Zoey and the MC are reunited, I feel better and am more relaxed about the next episodes. But I still think it could and should have happened sooner, at least in the "others'" direction.
I think this is kind of a short-sighted view, in all honesty. Do we really want all our MCs to be blank slates, amorphous blobs who have never had anything interesting happen to them until the start of the game? I personally don't think so. That would make a lot of the games much more boring. Player characters deserve depth as much as the love interests do.
By and large I agree with you that player agency should be more impactful than forced character backstory, but there will always be limits imposed by what is necessary for the narrative. To give an example, I've seen numerous people talking about this game gripe about how they wish they had an option to not join the DIKs because they were mad about the various hazing measures or thought Tommy was an asshole or whatever. Like, what? Did you not notice the frat's name in the title of the game? Joining is kind of the whole point. At a certain point, you can't satisfy everyone who's gonna play the game by giving them infinite choices to suit how they might want to play; hell, I saw one guy in another thread claim a game would irreparably break his immersion if he saw his character eating foods he didn't like because he would never choose to do that. And yes, that's obviously an extreme example, but I think it illustrates my point well. No matter how many choices you offer, no matter how insane the branching becomes, you can't make everybody happy.
The main problem with Zoey is that she isn't actually a character - she's a plot device. She exists to be a source of relationship drama in the second half of the game; the first half is all about the MC choosing whether or not to be in a relationship, but the second is about loyalty. And it's easy to navigate that, drama-free, if you can just ignore every other girl in the game. So here's one that, even if you have zero intention of dating her, will cause drama just by existing due to past history. Of course, the problem here is that you can choose to
not date any of the main girls - but if you do that, where's the drama? So it can't just be a happy reunion that causes current girlfriends to get suspicious, there has to be a whole bunch of mixed feelings so there's drama on the others route as well. This game is a soap opera, it exists to manufacture drama.
A big part of the problem with that, however, is that while Tremolo the character clearly feels lots of complicated feelings for Zoey... we the audience do not. We didn't experience his life. We didn't see the everyday interactions between them. We got glimpses here and there, but the majority of their interactions are in the interlude, which mostly focuses on her being on the other side of the country and which many people just kinda skipped because they were bored. So, yeah, we didn't exactly experience the conflicting feelings our player character did when she finally showed up again. Most people rejected her out of hand, and the people who did want to flirt with her weren't exactly about to do that while already on a dedicated route anyway, since we'd had 8 episodes to get to know the main girls and half of one to get to know Zoey.
I'll compare Zoey's introduction to the beginning of Fallout 4: our protagonist's spouse is murdered in front of them and their son is kidnapped, and now they have to explore the post-apocalyptic wasteland to get him back. That's a compelling narrative in game, but the player doesn't really have time to form an actual attachment to either one before it happens, which means that hey the time you have actual agency you don't really care about following the quest beyond some sense of completion.
I don't know at what stage of development DPC had all the Zoey stuff more or less finalized. I suspect he knew from the beginning he wanted to do the dramatic return of the ex storyline, but I don't remember exactly when the first mention of her was - I think it might've been at dinner with Bella? It's been a while since I played S1 though. But if I were to rewrite this game with all the knowledge we have now I would, among other things, give Zoey more prominence. Bring her up in more conversations, maybe have a couple flashbacks, that sort of thing. It might be awkward to fit in and make her eventual return more predictable, but it would give players more attachment to her as a whole.
I also think that starting the game at her departure, rather than in a random convenience store(DPC's favorite way to open games), would have been a great way to explain several of the weaker plot elements. Tremolo attends B&R not because he has a specific goal or path in mind, but because he feels like it; wouldn't this be better if he was doing it to find a fresh start after his first love moved away? He develops crushes on Josy and Maya regardless of player input - again a plot point to create drama; wouldn't this make more sense if he was just trying to rebound after Zoey left? His experience with Zoey would also explain his sudden need to make a choice at the end of Episode 8, something that a lot of people felt was forced and out of place; if it was triggered by a sudden reminder of how his relationship with Zoey ended before he could express his deeper feelings and a desire to avoid making that mistake again, wouldn't that have felt much more natural?
Obviously I know that's all retroactive, and a lot of media would be better on the second attempt once collective knowledge and opinion has been gained. But I do think that the core problem with Zoey's inclusion doesn't have anything to do with player choices surrounding her. I mean, think about it this way: let's say that when she shows up Tremolo has absolutely no prior attachments to her, meaning your interactions with her are solely down to your choices as the player. Would getting with her feel as meaningful? Or would it be a more shallow choice to pursue a woman you just met because she's attractive? That's a fine and dandy reason at the start of the game, when
every girl is in that boat, but halfway through the story? Doesn't work.