Can one say FPGA Replay is not a WinUAE in a hardware and that everything in it is actually custom chipset?
It's far closer to custom chipset than software emulation, if that's what you are asking. The FPGA simulates the hardware of the classic chipset directly (no software running on a generic CPU, but rather the FPGA re-implements the Amiga chipset), however the simulation is not the original hardware exactly (due to no-one having these details, and the gate level deconstruction of the original hardware is not complete yet) so there are going to be a few incompatibilities.
There are arguments about the meaning of emulation, simulation, etc, let's not go there again.