Okay, I finally had time to test this, just for someone who has the same problem as me :)
Some more information regarding this mapping thing:
https://learn.microsoft.com/en-us/windows/win32/winprog64/file-system-redirector
And the important part here:
PS C:\Windows\System32\config\systemprofile\.ssh> &"C:\temp\Winscp\winscp.exe" /keygen $env:windir\sysnative\config\systemprofile\.ssh\id_ed25519 /output=$env:windir\sysnative\config\systemprofile\.ssh\id_ed25519.ppk
Some more information regarding this mapping thing:
https://learn.microsoft.com/en-us/windows/win32/winprog64/file-system-redirector
And the important part here:
32-bit applications can access the native system directory by substituting %windir%\Sysnative for %windir%\System32. WOW64 recognizes Sysnative as a special alias used to indicate that the file system should not redirect the access. This mechanism is flexible and easy to use, therefore, it is the recommended mechanism to bypass file system redirection. Note that 64-bit applications cannot use the Sysnative alias as it is a virtual directory not a real one.