One question, what is the difference between installing SRCDS Non-Steam Windows (SteamPipe) U.P v1 update patch, and choosing "2" - Update into SRCDS Updater-Patcher?
You mean choosing "1" into the SRCDS Updater-Patcher. (^^,)
By choosing "1" into the SRCDS Updater-Patcher, you will update your server's files but not the extra ones.
By installing the update patches, you will update the extra ones. RevEmu, MetaMod and SourceMod.