Nowhere in this article does it suggest that the One will overheat. This is just an insurance measure, to make sure that there are no Red Ring like failures this time. Considering the Xbox One has a large open air design case with vents on half of the top, both sides, and the back, a pretty big fan covering the SoC, and no internal power supply generating extra heat, I don't think we need to worry about overheating, not even after the small graphics core clock increase, not unless you have your One on a very tight closed-in shelf, which would be your own fault.
If anything is going to overheat, it'll be the PS4, it's 50% smaller than the One, it only has vents on the back and very tiny vent under a lip on one side, and it has an internal power supply generating extra heat inside the case.