That, I cannot answer with any authority, but I suspect that much like the rears getting 5.1 upmixed to 7.1, the Atmos speakers will get used, even if not authentically encoded.
Perhaps somebody can confirm my theory?
That said, I am going to start buying some stuff just for the atmos experience when I get that part of my rig working. I have the AVR... and when my big speakers come in, I'll only be a pair of atmos speakers shy of the .4 rig.