The documentation is thin so let me add.
The purpose of SetCustomSettingDataGlobal is to save data in the XProtect server for your convinience. SetCustomSettingDataGlobal is independent of user, SetCustomSettingDataUser saves the data in the context of the current user. GetCustomSettingDataGlobal is used to retrieve the data from the server again.
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SetCustomSettingResultType ServerCommandService.SetCustomSettingDataGlobal (string token, Guid customSettingId, CustomSettingData customSettingData, bool forceOverride ) [inline]
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string token is the authentication mechanism, you get the token at login
Guid customSettingId is the identification you give your solution
CustomSettingData customSettingData is the data you want to save in the server
bool forceOverride overwrite previous data