But I think we'll get something along the lines: "We're not an authority on what's canon or isn't" in regards to that question.
Dark Horse doesn't need to be an authority in order to say what FOX thinks.
At least, it hasn't stopped them in the past.
The point is that just because one writer chooses to not incorporate a plot element from a source doesn't mean that source "isn't canon" anymore in the grand scheme of things - it just means that one writer is choosing not to let that source color the story they want to tell.
Case in point: the upcoming Predator comics not having Super-Predators, or 'Predators' not directly referencing the plots of the AvP movies, or the writers of the upcoming comics saying they weren't going to reference the old comics. That doesn't mean that stuff "isn't canon", just that the writers aren't saddling the new stuff with that baggage because it doesn't help them tell the story they want to tell.
AvP2010 referenced 'AvP' because Rebellion thought it would help their story.
I don't see how merchandise has any bearing on the canon or storyline of the franchise. Merchandise is something which fans buy to add to their collection.
It's also something that keeps a franchise in the public consciousness and reminds people that something exists. If FOX didn't want people remembering the AvP movies and all the things in them, why would they keep authorizing things from it and keep reminding people of something they want everyone to forget or ignore?
Compare it to, say, the Hish concept - evidently FOX literally told other EU writers to outright not reference the Hish concept. That could mean it's been retconned out of existence per FOX, but who knows?