No music. This is also a problem on Windows, not unique to Linux.

Same sky texture for all levels. I understand this is an issue with Windows as well, however. Also, certain text boxes, such as the briefings from the pause menu, are glitched out and unreadable, but this has almost no impact on the game.

Boot the game with num lock off. When I didn't, I found all keys were dual-bound to num lock, which paused the game. You can turn off num lock after starting the game, but it takes a minute before the other keys are unbound.

I had frequent (but not quite consistent) crashes when trying to start the final level, but they seemed to go away when I stopped purchasing the mortar before the mission. It's also possible that the upgraded mines or ksat buildings were the culprit or it might have been completely random. Consider avoiding the mortar in all playthroughs.