Have you seen the Advancement form that must be submitted to the council office? I have attached the top portion of it (less my personal information).
To order the Merit Badge I have to fill out this form and sign it. That puts my name on the record that I verified it.
Item 7 - I get to verify they are registered as a merit badge counselor. Below that, I get to certify that it's all correct and following the standards. Scoutbook is the easy way to verify this. If there is going to be a problem, I would rather find out now, then when the scout is applying for Eagle and the office is double checking records.
Before anyone asks, this form is populated from my Scoutbook account.