Not necessarily. FPGA cores are black box reverse engineered from the original hardware, which involved a lot of guess work and trial and error. Chances are there are some flaws that crop up in the process. The only way to get a 100% accurate FPGA core would be if someone used leaked HDL from Nintendo, which would be very illegal and would land that developer in court.

For example, I believe the Verilog for the N64, Gamecube, and Wii were all leaked in the gigaleak, but the person who developed the N64 core for the MiSTer never downloaded or read that code, and instead completely reverse engineered the original black box hardware to write his core. That core is not 100% accurate, and some games even require patches to function properly. Granted, that is more due to space limitations in the MiSTer FPGA, but even if there were no such limitations, it would be very unlikely that the HDL written would be functionally identical to the leaked HDL.