If you have a dozen layers and they each add 5% slowdown, okay that makes a CPU half as fast. That amount of slowdown is nothing for UI responsiveness. A modern core clocked at 300MHz would blow the pants off the 600MHz core that's responding instantly in the video, and then it would clock 10x higher when you turn off the artificial limiter. Those slight slowdowns of layered abstractions are not the real problem.
(Edit: And note that's not for a dozen layers total but for a dozen additional layers on top of what the NT code had.)
These are things we're unlikely to get back (and by themselves already make typical PC stacks unable to deliver smooth hand-writing experience - Microsoft Research had a good demo some time ago, showing that you need to get to single-digit milliseconds on the round-trip between touch event and display update, for it to feel like manipulating a physical thing vs. having it attached to your finger on a rubber band). Win2K on a hardware from that era is going to remain snappier than modern computers for that reason alone. But that only underscores the need to make the userspace software part leaner.
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[0] - Source: I'll need to find that blog that's regularly on HN, whose author did measurements on this.