https://bugs.winehq.org/show_bug.cgi?id=46072
--- Comment #5 from Tom B tom@r.je --- I have narrowed this down slightly with more luck than judgement. I tried running the game on my laptop and noticed that although the average framerate was worse I didn't get the stutter.
I did, however, get a warning from the game "Failed to initialize audio, do you wish to continue without sound?". I never use my laptop for anything but work so didn't even have wine installed. This was lucky as I didn't have any lib32 audio libraries installed either.
Thanks to the warning, I tried removing the Arch Linux packages lib32-libpulse and lib32-alsa-lib.
Again, I got the same warning when starting the game, and no stutter when NPC ships loaded! It is almost certainly an audio issue. I'll see if I can tweak the audio settings for wine or the game to avoid the issue while still having audio.
It explains why my earlier attempts made no difference, however. I must be something to do with loading the NPC's related audio (I'd imagine the engine noise).