I have *ONE* entity (an S-Corp) that doesn't have a set of books.  Granted, some of the QBO 'books' are often GIGO.... don't get me started.

The one without any set of books I enter the totals into a QB file I set up for her.  Income in, expenses per the excel spreadsheet, add/subtract a few things I know she doesn't put into excel.  She gives me the ending cash balance. 

Any difference - we sit down & chat about whether she took money out/put money in.   Usually the answer is 'nope, I didn't'   THEN we find out what income/expense figure is wrong.   

I 100% agree - there is absolutely no way to be sure all activity is captured without reconciling cash, and having a balance sheet.