[Baghi]

^ as of my knowledge, this is only happening to the Steam servers, i.e. the servers which we create using Dedicated Server from Steam tools. It doesn't happens in standalone servers (which are installed through hldsupdatetool). So I'm sure same is the case with Linux servers too.

edit:
I even tried to downgrade my dedicated server.gcf to an old build, and disabled "always keep this tool up to date" even then it updated it. ffffffuuuuuuuu