Voice lines may be missing during FMV cutscenes on audio interfaces that have some sort of surround support (e.g. Focusrite audio interfaces in my case). Use protontricks with winecfg to disable surround support on applicable audio interfaces and use Stereo instead (also consider disabling it on PulseAudio Output). Voices lines should be back after a few restarts (usually two).

Slight frame drops and stutters on screens and areas that have a somewhat dense composition, such as the Tartarus entrance, the fusion interface in Velvet, and during the door transition in Velvet, to name a few.

Some settings do not save, such as voice language. However, this does not affect the most critical settings such as display, graphics or sound, making it usable nonetheless.