You hide it in the terms of service and hope that the person at the company buying it bypasses official procurement (i.e. buys the software with corp credit card).
Where I work the procurement organization will required that verbiage is removed.
When have you ever seen Apple as a reference customer? This was probably some unfortunate Apple employee using their corp email account for the receipt to be sent to. It could have even been a retail employee, which isn't as much as an endorsement as an engineer working on UIKit for example.
I bet Apple didn't give them permission, they never want their logo to be used for marketing purposes for any reason. There are no takeaway Apple-branded gadgets for instance (while I have tons of tshirt/pens/gadgets with logos/products of any technological company in existence), and many shopping malls in which Apple has a store can't show an Apple logo on the big ads panels outside.
I'd love to actually know how Apple are using this , especially in what apps.
All apps I've seen come from Apple tend to prefer rendering resources using images rather than code, even where you might assume something is done in code to start with, at least on iOS anyway.
I suspect you can just add them so long as you don't have an NDA. It might result in losing them as a customer if they had an expectation of privacy (for example, if it affected one of their acquisitions) - but that's usually done through an NDA.
In general, do you have to contact companies and ask them permission before you put them on the customer list?