In a certain other college VN, Maya and Josy having parts of a scene and possible points connected to if you favored one over the other throughout the life of the throuple was one of the dirtiest moves.
That said, I'd be alright with some threesomes in Intertwined but I just don't see how a harem fits. Harems require communication or the girls to be idiots and while sometimes the girls are silly here, they aren't harem bimbo silly.
That was specially nasty, it gave us no warning...
Still, i can see something similar playing out with Alexis and Erynn, whomever goes into the threesome as the GF... ending up jealous and insecure of the chemistry between the MC and her friend.
A full harem wouldn't suit the game in any way, it would be ruining what the game has stood for...
Personally i love making these girls insecure and jealous of each other.
A throuple ending maybe would fit for Layla-Elena but that's it i think.