And if it is Canon which choices were we supposed to have made regarding the key plot points
Spoiler warnings, obviously.
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It's a fair bet that the ending where the team joins with Vauclair in his quest to kill the dragons is not canon; in this version of events, Dunkelzahn is killed before becoming president, which means he can't kill himself to prevent the Horrors from crossing over a year later. Not to mention all the other dead dragons this choice leads to.
Almost all of the the other endings are ambiguous enough to all have been possible canon endings, in my opinion.
Feuerschwinge could have lived or died and we wouldn't really know in 2075. If she lives, she essentially just goes off to sleep until the next age. If she dies, well, then she has no further impact on the world.
Panacea itself likely ended with the death of Vauclair, which is almost guaranteed (either he kills himself or Audran does). I don't think I've played through the game where Vauclair doesn't end up dead, at least.
APEX is another story; I'd say that from the purposes of canon it most likely was taken out. Otherwise, hundreds of deckers would have just up and died, as it had already begun it's rampage by the end of Dragonfall (Clockwork for sure, possibly Tolstoi as well; probably a whole hell of a lot more, including the team protagonist if they freed APEX but didn't give him control of the Panacea project).
All in all, a very few key events are (almost) impossible to include in the main storyline; the rest are pretty much all possibilities. Personally, I think this is a good thing.