Intel measure the TDP based on the base clock, yes. However AMD seem to measure it based on what the CPU is likely to draw with boost clocks over a sustained period of time, so their TDP numbers are quite accurate.
If you then compare the actual performance per watt, a 12 core CPU at 3.1 base / 4.2 boost pulling down approximately 65W is very impressive. Something similar from Intel (in terms of number of cores at even just the 3.1 base frequency) would likely have a TDP of at least 120W.
Closer, yes, but more useful? Both are off by a mile - not to mention that TDP isn't supposed to tell you a chip's maximum power consumption in the first place. It's supposed to tell you how good your cooler has to be to sustain base clocks / single core turbo, or in AMD's case, to sustain base clocks and some? boost clocks for a limited time.
>If you then compare the actual performance per watt
Performance per watt can certainly be interesting for many people. Performance per watt just isn't connected to TDP. The 3900X (105 W TDP) has higher performance per watt than the 9900K (95 W TDP). Probably at any frequency - although potentially the 3900X can't clock down as much. The 9900K can run Cinebench without a cooler after all (at least the 8700K can, so I'd suspect the 9900K can do that too), while the AMD processors can't. Also, the 3900 (65 W TDP) has the same performance per watt as the 3900X (105 W TDP), if you let them run at the same clock speeds.
The AMD power calculation is not "bit different", it's Intel who is cheating big time.
On a system with constrained power values, those who buy Intel will suffer a substantially higher hit than those who buy AMD.
I really, really don't see how. Both TDPs have very little connection to how much power the chips actually pulls at full load. 105 to 140 isn't useful in any way. If it was 107, sure, but 140 is 1/3rd higher than "spec" (I write "spec" because TDP isn't supposed to tell you what the highest power draw possible is if your cooling can dissipate more than the TDP in the first place, people just somehow seem to use it that way).
If you have a fixed TDP cooler, all you have to do is put that cooler on CPUs and see which ones will be faster. No looking at the specs required. If you have a fixed power consumption budget, but a better cooler, all you have to do is downclock until the CPU stays within that budget and then compare performance. Again, spec wasn't useful.