Hi Federico,
SQL Server 2014 and above or SQL Server 2012 SP2 and above is supported on Snapcenter for protecting your repository. sorry if the IMT was confusing.
Also, Protect-SmRepository can be used to protect your repository even if the server and plugin are on the same machine. The error you are seeing should be for some other issue and not because server and plugin are installed on the same machine.
Thanks,
Ujjwala