When it comes to the detailed timing and edge cases of hardware, especially peripheral hardware, software-based hardware emulators try to cover the most important cases. As far as I understand, an FPGA-based emulator would try to emulate the structure of the hardware, not its behaviour, thus resulting in more accurate emulation. Where do they plan to get information / documentation about the structure of the hardware? AFAIK most of the behavior is reverse-engineered by trial and error.