"No one has the original chip designs anymore, so the FPGA Amigas are workalikes, they do not behave exactly as the original chips. "
True, but they will be much closer than a software emulation. It is possible to get exact behaviour by running the FPGA core against a real custom and looking for any differences. This is what I've been doing with the Atari chips and will do for the Amiga customs. In this way you can prove the chips behave identically to the originals for all the stuff you have tried, demos, games etc.
If somebody wants to throw money at the problem it is very possible to reverse engineer the logic by examination of a real chip - you scan the chip, strip off the metal layer and repeat. These chips are old so the feature size is large, but it's still expensive.
But, you are right, software emulation is good enough for most things.
/Mike