I would say QBO is built more from a tax standard than a true GAAP standard that could hold up to an external audit on its own without manual work-arounds.  With any system, you have to make accruals, but QBO is a bit clunkier because they try to oversimplify through automation and the automation is hard to work around.  For instance, in my practice, I need to accrue revenue for unbilled time.  Just trying to figure out how to get that number into my financials in the correct spot (rolling up to AR) was extremely tricky and still doesn't really work well because it tries to force me to make a payment against the journal entry.  I have had plenty of QB specialists not understand the concept of unbilled revenue and accrual accounting.  Desktop doesn't have as much of a problem because it has more bells and whistles.  Technically speaking, if you can make a journal entry in a system, you can get it to GAAP.  

It may be easier to ask your coworker to give you an example and we can address it specifically.