Couldn't you argue that the minute he got amnesia, the "real" Geralt ceased to exist? That was the moment the new Geralt was born. When he got his memory back he didn't lose the new memories post-amnesia. The Geralt we control in W3 is a combination of the two. While it is true that "real" Geralt's true love is Yennefer, it is also true that "new" Geralt's true love is Triss. That is why we are given the choice in the first place - the current Geralt clearly has unreconciled feelings for both of them.
The 'real' Geralt ceased to exist at the end of the books (like you said), the games and their stories are told by a different author/s. Sapkowski said that the games and books are different, he even said "no mixing is allowed" . Just as you said, when Geralt regained his memories he had the experiences from the books, and the experiences from the previous games to influence who he wanted to be with, and since this is a game where we control Geralt and focus on his new story, there is in no sense having to choose a character because of a different medium (in this case - books) unless they like that character . If people choose Yen or Triss, you could argue it is because the player (us) likes that character more, it should never be forced or told that we have to strictly follow the books, heck if i wanted to do, what would be the point of playing through the games story. Anyway the point is that the character we play in the Witcher 3 is not the 'real' Geralt.