As a linguist, I liked the novel but I totally agree the "first contact" aspect is pretty shoddy. The microbes magic is like a necessary evil to explain why we suddenly can (and must) go interstellar.
The story also includes some "unaddressed magic", like how come Rocky find Grace "at" (orbiting) Tau Ceti? Like we would instantly detect an alien space ship entering "our solar system" because "we're there too".
The Expanse novels & series and Hail Mary have ruined me for fantasy-science-fiction. I love the idea of having one big conceit and then building a universe that is as consistent as possible with everything from known physics to known sociology and psychology given that conceit.
For the expanse it was fusion drives and the protomolecule. For Hail Mary it was astrophage.
Just like the magical linguistic tools of Hail Mary, the Expanse broke this a bit too with things like spinning up the asteroids without ripping them apart. But, these are still two of the best hard science fiction out there. Sorry Cixin, Remembrance of Earth's Past was fantastic but it quickly devolved into fantasy.
One note, I always thought the spinning up asteroids part of The Expanse was particularly unfortunate because the plot would have worked just as well with giant spinning stations on the asteroid surfaces to let the belters live in limited gravity.
The story also includes some "unaddressed magic", like how come Rocky find Grace "at" (orbiting) Tau Ceti? Like we would instantly detect an alien space ship entering "our solar system" because "we're there too".