I prefer to use drawing symbols (not notes) that handle integrated complex item and flagnote callouts along with off drawing PLs managed in Excel that are semi-automatically bounced against the model tree to allow validating all the parts are identified and that all quantities are accounted for. It makes it very easy to perform customer audits.
My preferred approach also doesn't answer the original problem, except to say, avoid BOM balloons.
To use the repeat region tables and BOM balloons is more trouble than it should be. Often it devolved into a Whack-a-mole style effort with balloons showing where they are least useful or refusing to show in desired views. In WF5 I frequently filed before showing BOM balloons as there was a 5% chance of software crash. It was the only operation that frequently crashed.
I would enjoy seeing the software development spec that backs up the current implementation. I suspect it has the words "scattershot" and "frustrating."