If you program an FPGA using the same HDL that was used to manufacture the original system then sure, it will behave identically (at least to the extent permitt

If you program an FPGA using the same HDL that was used to manufacture the original system then sure, it will behave identically (at least to the extent permitted by the laws of physics). However, if you are reverse engineering the chips and replicating the HDL without being able to peek at their actual circuitry, it is no different from doing the same in a pure software emulator from an accuracy standpoint. The only advantage of FPGA-based emulation in this case is that it can interface in real time with no latency to physical hardware such as game cartridges containing additional CPUs and whatnot - useful for consoles like the SNES, but such cartridges were not really a thing on the N64.