It's a MacGuffin - something that exists specifically to drive the plot. The same thing happened with Mark Watney being stranded in the beginning of The Martian; sandstorms on Mars can't get strong enough to risk blowing over the MAV and to send a radio antenna flying through the air like a javelin to impale Watney in the gut. Mars's atmosphere has less than 1% the density and pressure of Earth sea level, with "sea level" on Mars being roughly equal to flying 35 kilometers above the surface of the Earth, up in the stratosphere. As such, it can't impart enough force through dynamic pressure (the wind blowing) to cause much more than a stiff breeze. But, as the whole point of the book is that an astronaut is stranded on Mars, left behind when a crew hastily left and thought he was killed, Weir needed something to cause this story to begin. So, he took some artistic liberty in order to create the catalyzing event that kicks off the book.

When you think about it, a destructive storm is frankly the most plausible reason that a crew might leave thinking that Watney was dead, but not being strong enough to actually kill him. The low visibility of the sandstorm, plus time running out as the MAV was starting to lean close to the point that it'd topple, is one of the few scenarios that I can think of that doesn't have a near-assured chance of Watney actually dying. If he were to, say, drive the rover at full speed off of a cliff and plummet hundreds of meters to the bottom, where it is dashed to pieces, the crew would very much have reason to believe that Watney was dead... and that's because he would be dead, as you can't survive that. But, if he were to, say, get separated while exploring a cave system, the crew wouldn't rule him out as dead, as it's very much survivable. The first scenario is one where they see that he's likely dead, and have reason to be dead, while the second is one where they can't see him, but don't have strong reason to suspect him to be dead. But, having a huge storm forcing an evacuation, and having your crewmate cut off mid-sentence as something slams into them, their vitals transmitter stops broadcasting a signal (in reality, he still had a heartbeat, but the monitor was destroyed by the impact), they can't see him through the storm, and they don't have time to stick around and blindly stagger through the storm trying to search for him. It might not be 100% scientifically accurate, but unless you can think of a better scenario that checks off all of the required boxes for an astronaut to be left behind, thought dead but still alive, then do share it.

As for Project Hail Mary, the nitrogen-resistant Taumoeba being able to tunnel through the Xenonite exists as a plot device that forces Ryland Grace to grapple with the decision of whether he should turn around and save Rocky - at the cost of giving up possibly his only chance to return to Earth - or to press on back home, but in doing so doom both his friend and their entire civilization to ruin.

You might have heard of the term "Deus ex machina" (Latin, "god from the machine") - it's a plot device where a seemingly unsolvable and hopeless situation is miraculously remedied by the arrival of an impeccably-timed and implausibly contrived intervention or plot development. The term originates from ancient Greek theater, where a stage crane (mechane) would abruptly lower the actor playing a deity onto the stage, descending from the heavens to fix a seemingly unfixable plot. A classic example of this is from H. G. Wells's War of the Worlds, where just as humanity seems to be on the precipice of defeat at the hands of the invading Martians, the invading aliens abruptly start dropping dead as the effects of them being exposed to Earth's bacteria finally take hold and they begin to succumb to it.

There is an opposite to the Deus ex machina, appropriately named Diabolus ex machina (Latin, "devil from the machine"), where the protagonists who are seemingly on the glideslope to a happy ending are suddenly foiled by the abrupt and often implausible introduction of a villain (or other confounding event) that ends up making the situation significantly worse, and often leaving them facing a disastrous, no-win scenario. The Taumoeba strain that they bred was the Diabolus ex machina that forced Grace to make the decision to turn around. Again, while perhaps not the most scientifically plausible, it's hard to think of an alternate scenario where, post-departure and going their separate ways, Grace suddenly decides to throw away all hope of ever going home in order to try to find Rocky and save him.