I'd repeat what other have said: they wouldn't be leaving the Milky Way if they were just going to homogenize the endings. There would be no need to run away from the decisions players made in the trilogy if they decided to just make all decisions come out the same in the end.
Even in this new setting, however, they are still likely to ignore player decisions in the trilogy that many people would expect to carry over. Like the genophage. Are the Krogan in Andromeda going to be suffering from the genophage? I sincerely doubt it. Krogan reproductive rates were supremely broken in the trilogy. The genophage was a contrivance designed to create some kind of moral dilemma, science be damned. Are they still going to go on and on about this chip on the Krogan's shoulder when the entire context for the genophage and its importance to the story is gone? No. Most likely, the genophage just won't ever be mentioned again.
We are also likely to never hear of the Geth or Quarians again. They have already floated the idea of getting rid of one or more of the races we knew in the trilogy. Quarians are high on the list of those not likely to resurface. Instead of taking a trilogy decision into account, they can simply ignore it altogether.
Just because DA had its keep does not mean ME will too. They never left Thedas in DA. And they never wrecked the entire continent. Thus, carrying over decisions did not present as many obstacles. OTOH, the changes made to earlier stories never had the impact in DA they did in ME. In DA the import/keep feature merely effected which cameos you got. In ME the import feature had a huge impact one whether you could achieve peace between the Quarians and Geth and what the outcomes of the Rannoch arc would be. IMO, ME had meaningful choices, whereas in DA they were merely cosmetic.