CAUTION: Lots of high-level spoilers for Chapter 9 below; read at your own peril!
Well, in Mal's case it sort of makes sense if you assume that Mal really did have feelings for Amanda almost as strong as for the MC; just because Jaye is becoming a close friend that doesn't mean Mallory is sexually attracted to her.
Of course going with that explanation would open up a huge can of worms about Amanda and offers no explanation for why Mal would be on board with a Jaye throuple as long as she's clearly second fiddle, so... yeah.
Oh, while you're here...
I find it unreasonably amusing that we can now definitively state that this was NOT the reason for the long dev cycle.
I don't even like Tara and I still found her absence disturbing!
It's funny, I've been banging my head against a similar but more niche issue for ages now. The only way to commit to Mallory is to have sex with her in Chapter 5; if you send her away (say... because you don't want to give $#@%$ Amanda a peep show), game over. No matter how committed
the player might be to Mallory, the MC flat out refuses to address the issue at all unless he's in a post-coital cuddle. For extra irony, I can't even avoid the pre-dump sexcapade because, again, the only way to break up with Mallory is ALSO in the wake of the Chapter 5 sex scene. Unsurprisingly, Mallory wound up dumping the MC on my main run in because of the 'open' relationship we sort of backed into. The whole thing turned out to be a cautionary tale about bad communication killing relationships. That's a little
too realistic for my taste.
To see this whole mess echoed in the main routes, though, is just depressing. The sexless Mallory run is an extreme edge case. The throuple is THE mainline, the whole game is practically one long tease for it. I don't object to making the throuple hard to get, but if you go that route the logic behind the requirements really should hold up in hindsight and IMHO these arguments are extremely flimsy. As many have already pointed out, why is it impossible to achieve the same end result by being loyal to Mallory when she's the one who seemed much more open to sharing at every turn? At the very least you'd think it would be Jaye who calls off the open path, but no. Just as importantly, why would an MC who already turned down Mallory for Jaye WANT to open up for a throuple at this late date? It feels like the MC needs to be disingenuous to pull his mini-harem off: admit your interest in both girls and it crashes and burns, but lie about it then gaslight Jaye into thinking it's her idea and you're golden. I don't care for that at all. Then again I was never interested in the throuple so maybe I'm just not the right person to ask.
As far as the update as a whole, it was remarkably underwhelming. The only way this "wraps up the main story" is that it closes out the framing sequence with Walt from the beginning of the game; it sure doesn't do anything to bring closure to the events the MC recounted within that frame. I guess you could say the chapter sort of sketches out how the MC's romances will end up and where the Prizer lawsuit is going, but those sketches are VERY thin. Aside from the throuple kerfuffle and the truly surreal 'Jaye is kicked out of Harvard' subplot, I think we could have sketched these same outcomes ourselves at the end of the last chapter. I mean, cheating bad, puppy good, solo paths possible, villains probably going to lose (thanks entirely to Christian!) - it's all boilerplate stuff. What details did we actually learn in this update? Nothing. Even the new idea of Mallory having to go into hiding for her own safety is quite literally over before it begins. The sex scenes were fine, but they didn't exactly break new ground and nothing else actually
happened in the finale of the story. Definitely not what I would have expected.
Maybe the devs were never as invested in the story as it seemed early on, or maybe they just want to wrap this up and move on to their next game, but this was not a good place to plant the flag and call it a day. The story needs more than some ending slides to close things out properly. Involving the MC in the resolution would be a good start.