Oh yeah, clearly I did not read the article well. Still, it doesn’t mean what you think it does.
First, Yuzu is more of an alternative API implementation than an emulator in this setup. The stock Switch OS and API implementation have been entirely replaced with Linux and the Yuzu implementation of the API. Given recent performance uplifts in the Linux kernel, I’m not surprised that Linux+Yuzu beats the first-party implementation.
Second, the use of the word “emulation” in the above thread is really a misnomer: Rosetta 2, Prism and the like all perform what is called dynamic ISA translation. Yuzu need not perform ISA translation when running on ARM hardware.