"Agreed, it may not have been the EFB's this time but they are certainly certified by the feds under AC 120-76C."
Granted. Though, I'm not sure they consider these Class 1 or Class 2. Of the former, nothing of the system is certified, not the hardware nor the software. Of the latter, only the provisions for power and mounting are certified - again not the processor parts, the display formats, interfaces, nor the software. Class 3 on the other hand - fully installed and certified - hardware, displays, interfaces, software etc. No way are the iPads considered Class 3. It boils down to cost and if you're lucky, you get what you pay for.
AC 120-76 is an operational AC, too, so it pertains more to the operational approval to have and use than it does proving the equipment is sound and reliable. I don't know what the FAA requires regarding the paper charts and alternate means to compute TOLD numbers, but if the airline doesn't choose to have on-board paper back-ups - it's an expensive choice.