Galaxy?
Hmm if there’s a Steam_Api64.dll file in where Witcher3.exe resides I wonder if you might not have to add
[Steam.Log]
Silent=true
To the SpecialK config file to disable the Steam functionality, sometimes GOG Galaxy and Steam API files kinda both exists in either version of the game and that can be problematic for compatibility.
I’d try with GOG Galaxy disabled also but I think it should work depending on how it hooks into the API.
My own preference is to use the SpecialK stuff locally though as D3D11.dll or DXGI.dll and on that note check so that GOG Galaxy doesn’t have their own D3D11 or DXGI dll files already present if that’s a potential conflict as well. 
It gets a bit complicated if you have multiple API’s working like this where there’s Steam files even without Steam or GOG Galaxy in the Steam version without GOG running and then possible issues around if Galaxy has it’s stand-alone Galaxy 32 or 64-bit .dll files or interacts directly through their own D3D or DXGI .dll files which might be causing compatibility issues with SpecialK.
EDIT: Hmm maybe GOG Galaxy on the SKIF blacklist could also potentially help but the game would need to be whitelisted I’m pretty bad at using the launcher so not much I can contribute with for how to set it up or utilize it best here.
Since I’m more of a local installation user so that would mean either the latest stable or beta build and using that.
Latest beta files would be from that post, SpecialK64.dll as DXGI.dll or D3D11.dll which means the config file would be named DXGI or D3D11 .ini next to Witcher3.exe the main game .exe not some launcher exe or how it’s set up for the GOG edition if that differs compared to Steam.
Best to get the global launcher build working and possibly also without using these WIP builds though.
Something like that I think far as paths and everything.