That's possible .. but it still feels like there's either a big and very important scene outright missing, as that is just too much of a jump in information shared between those two - ooor Dots simply wanted to just avoid that scene altogether because how the fuck do you write something like that to sound somewhat believeable?
I mean hey, i'm not knocking him or the game. I just wonder if all the people praising the Update so much just celebrate the sex and dgaf about the story ... or if i'm genuinely missing some content here. And seeing as Jens underwear was mentioned and my day-counter sometimes didn't move (it's been Day 19 for three days! Groundhog-Day!), it felt like maybe an issue for a bug-report.
Maybe consider that Elena had essentially the same "reveal" of her knowledge with MC and D in two different scenes, as you had discussed earlier: I like when a story offers an organic interaction which is not fully expository and these scenes felt as such. Both characters knew Elena well, trusted her intentions towards them and even may have been intimate with her (depending on which path MC took) up to the point when she offered her personal, heartfelt and essentially send-off advice. She was telegraphing her approval of their relationship in almost a parental manner, curiously enough: because she was the only other person in the world who could possibly know and/or understand them at the time, perhaps.
An interesting parallel to their mutal accepting of Elena's understanding could be children whose parents formally plan to divorce: every friend of mine whose parents divorced has told me that they already knew it was going to happen by the time their parents decided to finally enact the process. In most cases, they had already been talking with one or the other parent in a manner which assumed it could be happening at any time, so would either avoid the topic entirely so that the parents could decide when to mention it or they would ask very explicit, previously unnecessary questions about logistics: is Dad going to be at my graduation?, etc. And, their parents - being so wrapped up in their sad, often bitter battles - would just respond or act in matter-of-fact manners, no longer concentrating so much on hiding the situation as managing the ensuing fallout. The kids knew, but weren't always confident about how to act on that knowledge.
In this case, Elena knew and appeared to be riding along with their moods and mindsets in a manner consistent with her "take charge, even if it might end up a mistake" personality, giving them a selfless push that only someone in her close, dual relationship could provide, I feel.
I can see your point, but in this case I felt it was a sublime move and actually brought in a dose of real-world interaction to the VN which D supremely ushered in during her magnificent "declaration of independence" that she had just given to Rachel. The final sexual climax was essentially another "organic" acting out of everything since D's break with her past, I feel: the rush to start a new life elsewhere, Rachel's parting blessing, their rush into MC's bed and that successful popping of the cherry which was the final loss of innocence and as their fantasy tale came true... so that the next morning a brand new story would begin. Their world has now grown into multiple possible paths and Elena's role was to both support them and get out of the way - she did her job beautifully. In the new view of their future, I see no reason why Elena can't be brought back in closely to their lives, but it will be a fresh understanding of where everyone sits in the relationship. Still, we have that damn picture of hers to worry about, too...