But my idea its not those endings would be basis of Andromeda's history. Would be nice just to see mention it, like Shepard's past (spacer, colonist, earthborn) based on PLAYER'S CHOICES. Its not canonise. But Synthesis would be impossible.
So players who choose Control or Destroy would get a nice mention, but players who chose Synthesis get, what, a middle finger? Like, "Yeah, sorry, we went out of our way to mention what those other guys chose but you chose something dumb, so we'll just pretend you chose a different thing..."
Seriously, that'd really break the immersion of the world, not to mention being pretty disrespectful to people who chose that.
You may not be saying they should make Control or Destroy canon but you are saying they should make it clear that Synthesis isn't canon.
If they can't reference all endings on equal terms, they shouldn't reference any of them.
And honestly, I think it's best they don't mention them as they should all lead to wildly different situations. Situations so different I don't think you should be able to "write around" them the way you can with other Bioware branching choices (like who leads the Krogan, who survived Virmire, etc.) That would minimise the impact of your choice.
But, like others have said, I think the most likely scenario is that the colonists in the Andromeda galaxy left before the Crucible fired (possibly as a project designed to save their civilisations). That respects all player choices and provides a direct link to the events of the trilogy without being beholden to it. If that's the way they go with it, I'll be really pleased.