Agreed on the way the strangling scene is shot; I could go either way on that though, just because the Yorha units are clearly designed to be hyper idealized "angels" of sorts, so pretty much anything they do is going to look intimate. The intensity of the scene could be reflective of their relationship, or the sexually charged imagery could just be "in the moment," so to speak.
The 2B/6O relationship just feels more textually romantic to me, I guess, because of the symbolism of flowers (the game even prods at this with Pod's observation that they are reproductive organs), the natural and open conversation they have after the sidequest, and the "thank you for the flowers" scene when the logic virus hits.
Really though, I think this is a case where we're probably both right, because it's not like characters can only have romantic feelings for one other character. Both the 6O and the 9S relationship are, if you'll forgive the pun, blossoming during the events of the game. There's no reason to think Yoko Taro couldn't have written a character who was starting to develop romantic feelings for more than one other character at a time; it's just that things go lopsided for 2B and everyone else before we get into boring love triangle territory.