The Mister SNES core has less accuracy like the software emulator bsnes, not all game work or there a bugs - they still "emulate" the hardware how they interpret it.
FPGA is just a different way of "hardware emulation" instead of traditional "software emulators".
The only real advantage of FPGA compared to software is the improved latency.
CPU based emulation will require a fairly powerful CPU just to emulate SNES. It's pretty expensive to emulate hardware in 180-190 ns increments.
At 13:43, he demonstrates a couple of snes games with effects that don't work well in software emulation (along with what the effects / game mechanics should be on original hardware). At 22:25 he shows these same games running on FPGAs (analogue pocket, mister) and behaving correctly, just like on original hardware.
As an aside, if this isn't the one you were referring to, it's still an awesome video by an amazing creator; I'm a big fan of this stuff after discovering it on accident. He gives a nice introduction to FPGAs in this same video.