I've since confirmed that the reply-to address is based on the email entered into the account settings and is not subject to SPF / DKIM validation. 

The emails clearly identify the business by using the business name in the From and Reply To fields (the from field just uses the intuit email so it passes SPF and DKIM checks.) And if the customer replies to the invoice email it will go to the email address configured on the account.

So basically you don't need to add Intuit's SPF include file or IP addresses to your SPF record or the key to the DKIM record. They do that for their intuit DNS entries. On some email clients you only see the From name and not even the email address (it's cutoff on my Gmail client because the business name is long.)

So what people are really frustrated with is although the name in the From field is the business name, the email address shown isn't their business email.

Intuit could solve this by giving everyone an spf include specific to the product and country affecting where the emails are sent from and a DKIM record. (Other QB threads have pointed out it has too many IP addresses to be compliant though.) But they realize this is going to be beyond the technical understanding of most customers so they chose a simpler solution. If people understand replying to the invoice email won't go to the Intuit email address then I think much of the complaining will subside.

I agree though it would be preferable that the from email address is a company address.