My response question would be that what scene outside of that flashback would imply that Maya and Josie had any feelings to rediscover? They spent a lot of time together in episode 4. Was there any interaction there which implied for longing feelings for each other, any hesitation or doubt in their interactions? And of course in episode 5 Maya walked away because it hurt to see a happy father and daughter. So considering the discussion with the MC afterwards, how would that discussion played out differently if it had been a random female student hugging their tearful father? Was there anything to imply that it was worse because Maya was jealous of the woman she supposedly loved? Or her being bothered by the fact that Josie literally didn't seem to care at all if Maya was there to support her?
I'm not saying that you shouldn't enjoy the threesome path or that you couldn't spin your own story to fill those blanks, but for it to be an argument for the story not being bad, at least for me, it needs to be supported by actual events in the game. And I'll be honest here, when I replayed it for this part, I tried paying more attention to the Maya/Josie interactions and I don't really know where a lot of the stuff suggested here was really indicated.
When the MC leaves the dorm room we see M&J having an argument but then when Josy uses that in-joke about giving a "diarrhoea shit" about Maya, it eases some of the tensions and they somewhat relax a bit. This, for me, shows that affection is still there because despite everything they've been through for probably months now, all it took was one jokey comment to put a smile on both their faces. If two people, be they lovers or friends, didn't still have affection for each other, then that in-joke would have fallen flat because it wouldn't be a happy memory anymore.
As others have pointed out, we don't see Maya and Josy together for much of that episode so we don't know how they acted when alone together, but they were probably at least happy to be back together, even if there was a tension between them knowing that they've been with the MC but that the other one doesn't know that. For all we know, they were probably walking on eggshells the whole time and had very short, stunted conversations where they were just trying to get along with each other and not get drawn in to any arguments.
I do think that some of the way it's been written wasn't very good, and you're right that Josy should have turned to Maya first before going to meet her Dad, but I think Maya's emotional reaction to seeing Josy with her Dad was on point and probably had a lot to do with the fact that it was Josy because this is someone close to her who is close to her Dad and it hurts more as a result.
Also, you're right that some of the stuff I say is "filling in the blanks", but that's how you critically evaluate a piece of work like this; you look at the characters, story, etc, and hypothesise how and why certain things are the way they are in order to make some sense of them. Some people might think it's a load of BS, but I enjoy it and sometimes it can be good to put yourself in someone else's shoes and think differently about things.
We gather they’ve had feelings for each other when they fuck at the lake.
Firstly, I always felt as though Josy in this situation was just giving Maya what she wanted and experimenting a bit with another girl and that the deeper feelings came later for Josy. Secondly, we know they made out but don't how far they went at that time or how far they've gone since.
Personally, I hope we get to have a conversation with them about this, maybe when they realise they can't fake a threesome for the Scavenger Hunt and decide they have to do it with the MC (at least on the poly path). Would be nice if, at this point, we could a nice, open discussion and find out just far they've gone with each other.