Lightning is software controlled smart port. It is totally capable of routing any signal the iPhone can produce. So a simple software update will support whatever changes to Lightning Apple introduces. When I plugged my Lightning headphone adapter into my SE, I initially received the message that it was not compatible, which required me to upgrade to iOS 10. That would not have been necessary unless Apple changed something about their MFi specs, as they already have published specs for Lightning audio. So it should have just worked. The fact that it didn't means Apple wasn't following their own MFi specs, or CHANGED them.
There is no difference in the sound from my headphone jack to the adapter. Since we know the iPhone 7 uses the same DAC chipset as the 6s, that would seem to suggest they intend to output a higher quality analogue signal than the iPhone 7 actually needs. The presence of 3 amps is highly suspect as well.