Before we get into FPGA -vs- Software Emulation we need to talk about whether or not FPGA is emulation when re-creating a system. If the device is truly a "clone" of another device it's re-creating and 100% compatible with it, then I am going to say NO, it's not emulation. Back in the day (and still today for that matter) we had PC clones -- not PC Emulators.
Here is the way I see it, take a CoCo3 motherboard, now re-create that motherboard using FPGA technology and recreate the analogue circuits with compatible parts such as the D/A converter (sound) A/D converter (cassette) and place the same I/O connections such as the cartridge port, joysticks port, cassette port, serial port, composite and RGB video output etc. Now you can take all your old cartridges the MPI, disk-drive controllers, printers, joysticks CM8 monitor, and boot DECB and it runs identical to a CoCo3. What you have is a CoCo3 "clone" not an emulation. EVEN if you have added improvements, faster CPU, more graphic modes, etc... as long as it remains backward 100% hardware and software compatible it is for all practical purposes a modern day CoCo3.
Same thing goes for a PC motherboard. Recreate a PC motherboard using one of the standard sizes w/ standard power connectors with all the standard connections to the outside world, PCI slots, SATA, USB, etc... re-create everything else in an FPGA, including the CPU, chipset etc ... if it is backwards compatible w/ say a 386 or 486, you have a PC clone, not an emulator.
Now take the DE10-Nano w/ the current MiSTer I/O boards, or take the CoCo3FPGA that runs on a Terasic DE1 (I would say even w/ the Analogue Board) these are Hardware Emulators. They are not cloning the entire system. I can't plug an MPI into the CoCo3FPGA or MiSTer running a CoCo3 core. Granted, some of these are a close call. Some of the arcades and others on the MiSTer are virtually indistinguishable with the real thing, nonetheless -- I still say they are emulating, and not a an actual clone.
There is a gray area where some things could be referred to as either. There is a fine-line where something is an emulation versus being a clone (or a re-creation).
I am going to say though that most of the time when we are talking about FPGA re-creations of retro systems we are in fact talking about hardware emulation and not clones. Because they generally "emulate" the I/O devices of the original system. The MIST, the MiSTer, the CoCo3FPGA, Roger's Matchbox CoCo and others are indeed hardware emulators.
Some commercial offerings might actually be closer to being clones, however since I have not researched them or owned one, I am not going to opine on them.