Honestly, I think the main "problem" is that it's the penultimate episode, DPC loves drama (especially leading into a Season finale), and without the loan issue there wasn't a ton of drama remaining in the throuple other than Maya and Josy's personal issues and how others (like parents) might react to their poly relationship. It would not surprise me at all if the JM drama this episode was to keep things from getting "boring", but it does also make sense from a development and narrative perspective to focus on it now that the loan is resolved. How many of the other main girl paths had some drama this episode? I've not played them all, but I know at least a few did so the JM branch is not unusual in that regard.
From a development branching perspective, having one "path" in this Episode for multiple different outcomes in future Episodes is efficient. It's easier to just have one path this Episode where issues arise and then perhaps split into branches later on depending on the resolution than it is to have multiple branches already where on one path everything's sunshine and rainbows and on the other path there's trouble brewing. This is particularly true since there's so much other branching already in the game.
It also make sense narratively to show the issues this episode no matter what. Regardless of if the throuple can be saved or not, the issues that could lead to a breakup have been there this entire time. If it can be saved, it makes sense to show the problems and then how they are "solved" rather than to just gloss over their issues entirely. Assuming the throuple can be saved, showing issues to resolve essentially shows the reader the "bullet" they dodged. Seeing problems and then saving the relationship can lead to a feeling of accomplishment in the reader, whereas not seeing any problems in the first place would not as much.
I suppose it makes some sense that DPC might have felt the need to inject some kind of new drama into things with them since the loan issue had now been resolved, and I suppose it also does make some sense that the new drama for them is to figure out where they go from here because the MC coming along has introduced an element to their relationship they didn't think possible which has confused and complicated their feelings for each other. It's also true, I suppose, that the relationshp with all 3 hasn't really been able to develop and flourish quite so smoothly because, at first, they had to hide it and then when it got found out, there was still the loan issue hanging over everything, and now they have a real chance of making a proper go at it.
If this is just going to be all about DPC showing people there are issues in their relationship and that whether you tried to keep things even or you favored one girl, either a little or a lot, the issues also relate to his actions within the relationship with a view to allowing us the players to have chances to set things right and ultimately achieve "success" with this relationship in the end, fine, and I hope it does, but this episode still doesn't feel good from the perspective of throuple fans even with all that taken into account, especially when it railroads you into a scene with one of them the way that it does.
Of course, this is the same dev that made AL, so who knows. Maybe he'll doom the throuple path no matter what again. I've already expressed my feelings on that here though, so won't repeat myself.
Well, I'll say my piece; it would be shit. Megan & Melissa never even got off the ground in AL, we weren't in a throuple for more than a few minutes in that game. Here, we're so much more involved and it's even considered a main branch to be with both of these girls. So if DPC doesn't allow for their to be a successful path to the throuple then he's just a massive troll for doing this kind of thing twice.