Thanks for the reply, but by "safe", I meant "will Steam not be found if I use Wine?"
As I do now, to be sure the games can be preserved without issues, I use a virtual machine that never had Steam installed.
But the process is extremely demanding for both time and processing power of my computer, so I was considering using Wine instead of virtual machines for testing these games.
But then there's the issue that my Linux install already has Steam installed, so I fear it might temper the results, making them not reliable. Thus the part about the multiple Wine/Proton prefixes being isolated.
Also, each Wine prefix does have files that simulate Windows' registry. It's the .reg files in the root of each prefix. (and I know Linux doesn't use registry like Windows)
Well isolating wineprefixes doesn't change much unless you've got Steam installed on some of them while others not.
It won't change the fact that any Wine "isolated" software can still escape Wine bounds if you don't remove DEFAULT SYMLINKS to your root complex of an underlying drive (these symlinks are there by default even tho they are COMPLETELY unneccessary for 99% of use cases, which means whatever software you run on "default settings Wine" can totally access ALL your Linux files no problem).
Wine is not a security sandbox. It offers NO SECURITY ISOLATION CAPABILITIES.
The bare minimum you should all (and I mean ALL) of you do is remove those default symlinks, on literally EVERY wineprefix that does not otherwise need them (they are barely ever required for anything).
Even if you do that there are still certain methods of escaping "Wine chroot" (for a lack of a better term, not sure if "root complex redirection" is a term that should be used here).
Speaking of which, I find it pretty mesmerising how seemingly majority of users of *NIX seem to still think they are "safe from Windows malware" while they use Wine.
Wine can run Windows viruses pretty well, and system call translation makes you automatically suspectible to the viruses doing harm to your *NIX install solely because they run in Wine.
On top of that default Wine installation system-wide settings are profoundly permissive, with things like automatic launching of exe files in Wine upon doubleclick being most-distro default.
would software be able to escape bounds of Wine? Generally yes. Under default symlinks: 100% possibility.
Would it do that? Depends on the software.
Would it recognise Steam install of another OS (as within Wine it is Windows and outside it is Linux, which the Steam clients are not 100% the same file structure wise)? Hard to say.
Out of curiousity:
what hypervisor do you use (and what host system)?
Do you PCI-E passthrough anything?