It's hard to say how much effect one way or the other this would have without doing tests on multiple samples with and without the mod. Yes, it spreads the heat out more instead of being focused around the CPU, but it also helps transfer it to the case so it can dissipate, so the overall heat will be less. And without it, that heat will eventually move to the battery anyway. And yes, it's going to spread throughout and radiate from the case once it gets there but, again, this would happen anyways, and I would expect it to have a net beneficial effect.
Still, the point isn't so much whether the mod itself is ideal, but the fact that Apple could have designed things better in the first place. They could have used thermal pads (or just shaped the interior of the case to make contact on its own, which would be even better) in addition to other improvements to help prevent those other issues, like using move heat-conductive case materials in areas leading away from the battery and less conductive materials around the battery, and by building a poorly heat-conductive barrier internally between the battery and the CPU. The fact is, it was already known the CPU is thermally limited, and this mod proves that with minimal cost and effort that could have been improved fairly significantly. Not to mention an optional limiter to throttle based on battery temp vs CPU temp.