And yet, I expect that is exactly what will happen. The translator tool will figure it all out for us.
My guess is that we'll find some kind of galactic rosetta stone equivalent relatively early on to give the translators something to work with. Ultimately, they're gonna have to hand wave it one way or another, 'cause otherwise we won't be able to talk to any of the new species we encounter without years of painstaking work, assuming understanding is even possible.
I'm still hoping we get at least one 'Darmok' questline, though. Star Trek is one of the oldest and most famous examples of the 'universal translator works on everything' phenomena - for good reason, as the show simply wouldn't work otherwise - and yet they still found a way to explore the fun dramatic potential inherent in the idea of having to work around the limitations of language to come to an understanding.
It'd get incredibly tiresome if every single first contact revolved around the concept, considering how often they're likely to come up in a game with a set-up like Andromeda's, but it's an idea worth doing at least once.