I went back and gave the game another try, and it actually seems to be running better now! I'm not entirely sure what changed, so it might have just been something on my end.
That being said, there were still a few performance hiccups. When playing as a runner, the game still froze for about 1–2 seconds whenever the ship fired its cannons. As the hunter, it nearly crashed when I switched to the cannon camera, although I couldn't seem to reproduce that issue on my second playthrough.
Hope this helps.