This might help.
Move SS2 out of Steams reach and run programs with Wine always in the terminal to see what's going on, like:
wine SSTool6.1.exe

While it is not advisable to run stuff like this with root permission, it was the solution for this guy.
SSTool should be trustworthy, but I repeat: Do this at your own risk.

Edit: What does the terminal output of wine say?

Again, no dice with root permission.

You may need to set up a wine prefix with various components enabled for networking to work properly.

Lutris (recommended) and PlayOnLinux can both do this for you. Lutris should have a game profile for SS2 which will set up a specific prefix with the right configuration to run the game with newdark and ss2tool, which is handy.

In fact, installing SS2 via Lutris (I'd recommend the gog version and bypass steam entirely) is recommended. The Steam and Gog versions both come with their own wine prefix already iirc, and Lutris should allow you to run ss2tool within the context of that prefix using the context menu, rather than using your default system prefix.

I use the gog version because I like managing the wine prefix myself.

For steam, which manages it itself, you'll need to manually run ss2tool inside that wine prefix

You can find online how to switch to a prefix and run an application within it.

Note that Steam does NOT run ss2 through proton, it actually just runs a wine prefix because a """"Linux version""" was released long before proton existed.

If you want to run it through proton instead, you can use steamcmd to install the windows version and then run it normally, which will use proton.

In my opinion, the company that manages the Linux version (night dive?) should just remove the Linux version from Steam entirely, since it's just a wine prefix containing the Windows version anyway, and instead everyone should just use the proton version, since tools like Lutris can manage it easier and there's no need to have an extra installation of wine lying around.

I might ask for this on the steam forums

But I digress. The Steam version has no copy protection at all and you could install it using, say, Lutris and pick "gog" to set up the profile, cancel the install and manually copy over the steam files instead