Thanks, but it doesn't seem I missed anything, honestly
Emily has discovered a bisexual urge she didn't previously express or experience - The Forbidden One path made that highly clear, actually. Let's recall that the different paths aren't completely different universes with alternative versions of the characters, but the same characters reacting to unique combinations of circumstances from the MC in their own ways. So, we already know that Emily in the Harem path is partly falling for Jenna and the feeling is mutual - we saw that in TFO.
At the same time, I think we both generally agree that Emily realized the MC should be as free as her to be intimate with the others. She's probably not just "feeling bad" from being with Jenna while the MC was (in theory) not given explicit permission to sleep around, but she's simply realizing it's selfish to keep that situation going (which is her conscience at work, plus consideration with perhaps Jenna reminding her) AND she's falling for Jenna. So, she likely doesn't *want* to have the MC think his life is all about her any longer: she's gotten the taste of being with another (woman) that she loves and wants that to continue as part of her life. She's probably angling for a multi-marriage arrangement as we've seen in other paths with characters who were not her, it's just that in the Harem path she would now be one of the shared spouses.
So, all the clues to Emily and Jenna's mutual appreciation for each other has been available in multiple paths by now: while I think it's valid for you to not like how they've changed with new experiences (i.e., that's just personal taste), I happen think it's been really cool to see them literally evolve before our eyes in this and other paths.
When the MC and Ada come home during the Harem path, it'll probably be some feeling out amongst them before everyone gets going in the same room together: Emily, Jenna and the MC all have experienced intimacy with other characters and now have multiple loves in their heads and hearts. Again, the other paths are clues to their malleable affinities here, but coming to grips with it together will probably take some tentative steps, maybe setting some shared expectations and getting each other up to speed on their latest feelings for others, etc. before they ever become a house of anytime, anyone, anywhere sexings that is equally understood and accepted without confusion or misunderstandings. Although, given Luxee's way of being so concise at times, that could all happen in a single release ...
This is all consistent with my prior post, IMHO.