Well, all I can say is... this is a bug.
I would assume that based on the ReloadFromDisk method, it would perform the same action without popping up a dialog. Please consider fixing this so it can suppress the dialog in a future version of TestStand or change your documentation. I know that NI can do this because for some reason, the same logic that you describe for the users file (race condition) does not seem to apply to the station globals file.
When I do a CommitGlobalsToDisk, I set the promptOnSaveConflicts to false and then I do a ReloadGlobals. Everything works fine without any prompts.