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If you create several queries in a row in a clean workspace, you can get several progress dialogs at once - one for each one, and it makes you think you need to check always sync in the background on each of them, which creates a negative experience for new users. It would be nice if this could be prevented somehow, but I don't have a good suggestion other than always syncing in the background by default.
I don't think new users are likely to create several queries in parallel. The overall experience could probably be improved by aggregating progress in a single dialog or by changing the platform default as you suggested. Since this UI is provided by the platform I would recommend filing a new bug against the Plaform/UI.