I'm this case the frequencies are similar and so wall clock time reflects the IPC difference (also, the two CPUs take the same code path, so the I is the same in this case, which isn't always true).
That only really happens on laptops, which can't dissipate as much heat as desktop systems due to size constraints. On a desktop, if you're using even AMD's stock cooler, you won't thermal throttle. That is, if you don't overclock.
Modern processors with boost configurations are rather complicated about "thermally throttling". These days with AMD's stock coolers you will be able to at least get the sticker speed on the CPU even at 100% load for a sustained time. Chances are, you'll actually get some % more speed than the sticker as it will usually continue to boost as long as power delivery and temperatures are stable. So even with an entirely stock configuration, a better motherboard and cooling system will overall net you more performance. This is without doing any traditional "overclocking" and just going with the settings designated with the CPU and motherboard. This same idea also applies to most of Intel's parts as well.
That's the same thing. Intel calls their stuff a dynamic boost so that some of their measurements like TDW are for lower clocks. Both CPUs end up scaling their clocks to a wide range.