The difference between a simple software emulation of a system like this and an FPGA simulation is that the software parses the machine op code and either explicitly or implicitly modifies the emulated machine state. A FPGA uses analogues of the original gates to parse and execute the opcodes so it stands a better chance of doing that the same way, and writes its states out to physical flip flops (in the case of its registers) or lines connected to a physical RAM chip.
But personally, for my needs, an emulator is more than good enough for my needs of emulating preexisting software, and maybe a little light BASIC coding. For people that are developing their own software and need timing information I can see how it might have more value, but anything you coded using that probably wouldn't work on emulators of the day until they were patched, and the nature of an FPGA means it's still not quite the same as the real thing - I assume you don't implement the clock edge detection that converts the wave form of the quartz clock crystal into a series of pips that start and keep the processor going, and there are other facets of the FPGA that aren't going to be quite the same as a CPU made in the 1980s.