I agree that this is not likely to end well for those who open their company files to Intuit, which is exactly what they are doing by logging into an Intuit account while opening a company account. And the folks who currently use Quickbooks to provide their payroll or ACH functions would do well to drop Intuit and get those services from other vendors. 

I have several company files. One of those needs payroll services and we contract to ADP for payroll. Not need to be logged into either Intuit or ADP for the payroll to work just fine. Several of our other companies use ACH (direct deposit) services. We do that through our bank. Again, no need to be logged into Intuit or the bank for that to work just fine. 

You have no need to be logged into anything else to use Quickbooks Desktop to do basic accounting, or even more the complex accounting  for governments or non-profits. It's all in the chart of accounts.