I haven't seen anyone do that, yet. I've seen a few people use the old method, which involved cross-drilling a 1 mm hole in the baseplate of a HSF.
There's going to be an impact, for sure. It'll probably be small, but it'll be there. Assume a 1 mm thick IHS (there's very little data available on it). The round hole area is 5mm in diameter, and 0.75 to 1.0 mm deep.
It's interesting that AMD would recomend that; I would have hesitated to leave a 5mm round hole right smack in the middle of the core.
As for a TEC, I'd assume that you have a 1/4" thick coldplate? The impact would be smaller there. I'd bet on this method being more accurate than the mobo, but I'd try to keep the hole diameter smaller, or even better, don't make a hole, just use the 1mm wide channel.
The problem with mobo readings is that there is no calibration, and there's a wide variance in actual temperatures. You can assume a 10 deg C (up or down) variation. It works well enough to protect the CPU, for which it what it's intended.
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