I always forget the name of their species, but the people who require a breather to pump in fresh non-Oxygen rich, I assume that if they had any ships, their life support would be exclusively their air, with those neck devices to help pump when visiting other plants and ships.
The Barzan! This is actually something in Discovery! They go to a small Star Fleet ship that was run by an all Barzan crew (just one family), and the atmosphere is modified for them, so the Barzan member of Discovery’s crew doesn’t need her breathing apparatus. I think you’re probably absolutely right that other Star Fleet ships are made with serious accomodations for other species. Maybe the Bolian ship has especially robust plumbing lol
They absolutely talk about the ships that just got totally owned by whatever science mystery they were working on. Like 30% of the Next Generation is: The crew of the Enterprise stumbles across an empty Star ship, or an abandoned outpost, and have to figure out what happened (and stop it from happening to them!)
The Fleshmancer in Sea of Stars is pretty terrible. He creates giant, potentially world destroying, monsters that feed on different types of despair, and so seek to create those emotions in as many people as possible. He committed one genocide against an entire race, and then trapped them in living death, unable to be seen, or leave his lab. He seems to have committed another genocide, just to make a birthday present for his friend. And this is all on just two planets, when he is acting in the same way across the entire multiverse