I doubt they'd be all that unfathomable. We come from the same universe after all, and as far as we can tell it's all governed by the same physics. It stands to reason that life on their worlds would have developed under at least some of the same rules we developed under on Earth. That should put at least some constraints on their forms and functions.

They might have learned different things than we have, they might know a lot more about our universe than we do, but I'd guess that much of what we've managed to learn so far will still be a part of their reality regardless of their level of familiarity with it. For example, more than 90% of the atoms in the universe are hydrogen. They might have discovered things that are more exotic and never seen on Earth, but the hydrogen atoms we've studied won't be any different from hydrogen they'd have studied. We share a home. By the time they've figured out enough of how the universe works to reach us it's pretty likely that we'll have some common ground to talk about.