Smoothing out minimum fps while killing mimics.
Nvidia has posted a hotfix driver, version 382.19, to their support website. Note that this is not a WHQL release, and the only note is that the driver resolves the stuttering issues 'some' users are seeing in Prey. This happened despite the previous 382.05 drivers being 'game ready,' though I should also note that Prey is an AMD promoted title, with Ryzen and Radeon logos splashed onscreen while the game loads.
Most driver updates from Nvidia come via the GeForce website, or through GeForce Experience, but if you're playing Prey on an Nvidia card and notice the stuttering, you'll have to manually update drivers.
I can confirm the stuttering problem occurs and is particularly noticeable when using the very high preset on every Nvidia GPU I've tested. Average framerates hit Prey's 144 fps framerate cap (which is a whole topic on its own—haven't we learned framerate caps are a bad idea yet?), but minimum fps even on high-end cards like the 1070, 1080, and 1080 Ti will dip well below 60 fps.
Update: It appears the secret to removing V-Sync is to disable V-Sync in the Nvidia Control Panel, and enable V-Sync in Prey. Go figure. Unfortunately, this does not work for AMD at present.
Parsing the data for numbers, with the 382.05 drivers, the 1080 averages 138.7 fps but has minimum 97 percentile averages of 60.7 fps, and dips as low as 10 fps. With the 382.19 drivers, the game averages 141.5 fps, with minimum 97 percentile of 82.8, and an absolute minimum fps of 25 fps. The story is the same at 1440p if you're wondering. Before, the GTX 1080 had performance of 105.4/48.4 fps, and with the new drivers it gets 104.9/77.3 fps.
There's still a lot of jitter in the frametimes, but the stalls aren't quite as noticeable. Hopefully Nvidia can continue to improve the framerate pacing with future drivers. But if you're playing Prey right now, especially at higher quality settings, the stutters are very noticeable and I recommend installing the hotfix.