My advice typically is that if you enjoy using an emulator then you don't have a reason to buy an FPGA based system. They are definitely less compatible and this will very likely stay that way for a while. The tg68k CPU core we all use is not cycle exact and probably cannot be made cycle exact. But that's what you need for a perfect replica. Someday someone may write a cycle exact 68k CPU core but this won't happen over night.
An FPGA board is perfect if you want a dedicated small box sitting next to your TV which you switch on to play quick round of rtype with some friends while waiting for a soccer game to begin. It gives you back this instant-on experience. And it simply doesn't feel like a PC and you'd probably never ask your friends to join you in front of a PC for some quick retro gaming fun. It's so small and quiet your wife won't even notice it next to the TV :-)
It's somewhere in between real hardware and PC based emulation.