because some Yen [and Triss] fans have already made their choice even without playing the Witcher 3
Geralt did, more than once in the books and even at the start of the game. Geralt offered the Wild Hunt his life in exchange for hers, so without that exchange the games wouldn't even exist in this form and he wouldn't have amnesia in the first place. So basically because he offers his own life for Yen, he makes it possible that Triss gets a chance, kinda ironical.
And those "you can't ignore the games"-argument. Yes, we can't ignore them, but it isn't the first time that Geralt had some kind of "replacement", so it's not exactly new for most of us and we all know the outcome from that and so does Geralt now.
It should be also common knowledge that he thought in TW1 that Triss is his former lover and yet nobody corrects him, so if Geralt thought Triss = Yennefer, is he really loving Triss then? He just mixed them up, because nobody is telling him who the heck Yennefer is.
I played both games once before i read the books, so i was in the same situation as Geralt. I had "amnesia" and i couldn't remember anything from the books, so i didn't know who Yennefer was exactly, so of course i went with Triss. That was just my "natural reaction" to all of this, i never really questioned the relationship, because everything seemed like it was supposed to be.
She seemed nice and i didn't really thought much about it or the consequences, but after reading the books, this matter gets a whole new meaning.
So i think this must be the same for Geralt now. He didn't really know who Yennefer was in the first 2 games until the very end, so he went with Triss (no matter what you did in TW1, you end up in bed with Triss at the start of TW2 and you are in a relationship with her, so that's canon from the games, everything else is variable), because he thought that was the status quo before he had amnesia, so did i as player, but then he realizes later that this was not really correct and thus the conflict arises.