FPGA mimics hardware 1:1 without overhead, which is why it works well. This is talking about software emulation, which has to use lots of shortcuts to make it fast enough (for most machines). The N64 has a weird architecture though that makes it difficult to find shortcuts that work well.
I did some FPGA programming in school, so I totally get it. The hardware is really amazing, but the janky proprietary development toolchains not so much. Plus, Verilog is kind of a pain in the ass.