They supposedly use Keynote, but I think with these presentations it's more likely custom motion graphics in After Effects or possibly Final Cut Pro if Apple is imposing in-house software.

Apple have an in house team that specialize in just these kind of keynote slides. I imagine it's worked up mostly in keynote, maybe with a bit of extra software like After Effects on the side.

They employ an outside company to do the bigger CG graphics, promo introductions and renders of the devices