Actually it may not be totally wrong, the form factor inside could be laid out differently, the microphones are in a different spot and it may not even be the mic itself picking stuff up from the speakers directly? The vibrations (which is how a microphone works) may travel differently through the frame of the iPad which inadvertently gets picked up by the microphone. FaceTime may be able to cancel it out as it may have some sort of programming that is built into it to give it a short delay from the time something plays to cancel it out or another way, but that being said, other iPads have their speakers and mics in different spots so it may just not be picked up as sensitively as the new iPad Pro’s.
That at being said, it’s not only the iPad Pro’s as I have had people complain about this from time to time on my iPhone as well. It is a software thing as it can be programmed to remove it as shown by FaceTime being able to correct it. I have never had anyone complain with FaceTime but many times coming from Skype.