Want to have it collecting dust in a museum? Sure, you're going to want the original. Nobody is interested in an FPGA for that.
Want to actually use it? If an FPGA is close enough that it is literally impossible to tell the difference in a black box comparison, for all intents and purposes it is the original. Emulation simply isn't accurate enough for that, but FPGAs can be 100% cycle-accurate. And this means you don't need to risk wear or damage on your genuine C64 just to experience what it is like to use a C64.
Emulation is very close to 100% cycle accurate for many, many machines. You would practically not deal with this problem anyway. Now, I may want to tinker with my computer on a board level, making a period-accurate hardware-tweaks for the machine, how exactly I'd accomplish that, if everything is just a big FPGA?
Now, having IC'level FPGA substitute for big chips on the original board is a bit better than one big flat fat IC, but it still a different machine and cannot be called C64, as much as a Ford-T is not a Ford-T if you put a modern electric motor to it, even if you tweak it to sound and handle exactly like T does.
Want to have it collecting dust in a museum? Sure, you're going to want the original. Nobody is interested in an FPGA for that.
Want to actually use it? If an FPGA is close enough that it is literally impossible to tell the difference in a black box comparison, for all intents and purposes it is the original. Emulation simply isn't accurate enough for that, but FPGAs can be 100% cycle-accurate. And this means you don't need to risk wear or damage on your genuine C64 just to experience what it is like to use a C64.