The Linux native builds tend to be a version behind or have poorer support than the Windows ones. It's based on the devs, of course, but the take away is that it's historically been a crapshoot.
SteamPlay/Proton provides native or better performance over Windows for what I play. I've been using it so long that I actually don't know which games have native Linux versions anymore. It 99% "just works".
VFIO is virtualization where hardware is passed through to the guest OS. I use KVM+qemu on Linux and attach PCI devices like GPU and storage to the VMs. This is a native Windows game build on a Windows VM on a Linux host. It performs within a tight few percent of bare metal Windows, and the host is fully functional while in use.
Linux gaming options range from direct and inflexible, to feature parity with native performance and compatibility, to complex but guaranteed native support. I've relied on the first and last less and less over the years as Proton has improved.
How about displays, though? It doesn't seem like you could have a proper integrated desktop between host and VM when using VFIO.
You can also connect the graphics device that's passed through to an external display.
As an example, my SO and I can both play a multiplayer game from the same computer this way. I can use a VM with lookingglass on my Linux host while she uses a monitor connected to the GPU her VM has attached, along with a passed-through hub with mouse and keyboard.
It helps that Threadripper has two NUMA nodes, but it's possible on any system with good IOMMU grouping.
You could also run regular multi-seat Linux with such a setup.
It should also be possible to do it without multiple GPUs, but that's unfortunately more involved (if anyone has a simple way to do this in wayland land, I'm all ears!).
Your understanding is wrong. It's largely a reimplementation of Windows APIs. Those implementations can perform better or worse than the real thing depending on quality of implementation and the underlying OS.
Some games will perform better on Linux. Some will perform worse. Some are about equal.
System calls are also something that would require an additional layer, as the required Linux system calls need to be made in addition to intercepting the Windows system calls in Wine code. Some other APIs in Wine may also be implemented on top of corresponding Linux APIs rather than just being standalone replacements for Windows code.
The majority of code in Wine is probably just reimplementations of Windows APIs, which could be thought of as being parallel to the Windows implementations rather than layers between a Windows API and a Linux one, so you're correct there.
I'd generally expect there to be a performance hit on average, but as you said, it doesn't always happen, and it's not as large as one might expect if thinking about an emulator or something similar.
I run RDR2, Fallout 4, TW series, and some indie stuff at those specs and I have no problems even with mods.
I see no difference from Windows but, ofc, you mileage may vary depending on your HW and what you want from your games.
What do you mean?