when the workbook kicks off it's scheduled extract refresh, then each data source have 2 hours (background query limit) to process.
For your second ques right now there is no option to set the backgrounder query limit for specific jobs.
Yes, it applies to each datasource. You can change the backgrounder query limit tabadmin commands if you feel it is insufficient.
And there is no option to set query limit for each datasource as of now.