Is this your first Witcher game? CDPR has always either sidelined or outright rectcon'd away choices between games. For example you are always with Triss in Witcher 2, regardless of whether you exposed the Lodge and the Conclave was reestablished in Witcher 2, Radovid always starts Witch Hunts, Anais never plays an important role, Iorveth and Saskia don't even show up, etc. They're going to canonize some stuff when they move forward, it's what they've always done.
"this is what they've always done" - done it only twice, can't really call it a trend or something they will keep doing nor should they. Its one of the biggest complaints how TW2 choices aren't properly respected in TW3 or affect the game's world, and they never said that they are consciously choosing what is canon and what isn't and making player's choices in many cases irrelevant or not matter or retconning them.
It's also a practice players should be against and not support dev in such design decisions. There is no canon in TW3 as of yet, that's for sure. If TW4 comes out and they decide that one choice is canon because of budget or time reasons or what not, then you could say "well they made X choice canon, sigh", but right now there is no choice that is predetermined to be canon, and from a player's perspective all of them should be canon and respected in the next game, whatever it might be.
Again, most of us are not fans of how as you say Iorveth and Saskia didn't show up etc, but i totally think the way they did it going from TW1 > TW2 is reasonable, since it was a low budget game and for them experimental - when they made it they didn't know if they gonna make another game, didn't really look that far ahead. And not many people played TW1. I mean even Dijkstra was in TW1.
And even in TW3 I don't think they canonized specific choices necessarily (regarding tw2), they simply ignored or didn't put the appropriate dialogue/events to represent certain choices for budget or time or design reasons. Remember, Iorveth was originally planned to be in the game and was part of the cut content.