The Holly Trinity and Lena/Holly are "pure" relationships that make Lena want to dedicate herself to it fully instead of fucking around. All the other instances you mention happen before the trinity or relationship with Holly are fully formed. They're also all casual flings or far from serious, so there's no reason for them to affect Lena's attitude towards yet another hookup.From what I could see, the Emma x Lena scenes in this last chapter can’t happen if the Holly x Ian x Lena trio exists...
THAT MAKES NO SENSE!! Why are some relationships randomly blocked like this? Lena can have relationships with Marcel, Mike, Mark, Robert, Stan, Ivy and Louise, but for some reason, the relationship with Emma is blocked because of the trio? Why weren’t the others blocked too? Some decisions in this game make zero sense!
There's currently single exception here, and that's Lena giving in to Seymour during the business trip, even if she's on the trinity route.