I understand that logic and concern, indeed I have fallen foul of that but luckily do know an amount of Excel that I could unravel, in fact in one instance I ditched what had been done and recreated the entire year from the bank statements and the invoice files, seemed simpler and quicker action to take.
However, using a sector specific product does make sense even if they know how to charge for all the reasons you cite, although certainly not worth the cost for tiny parishes in my opinion and experience. My aim is steer the council away from their misguided love of Quickbooks, Sage and flippin Xero accounting....