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The reality is that the vast majority of these FPGA-based clones don't actually perfectly emulate the logic. They're using the same reverse engineering techniques the traditional emulator developers used and sometimes even the same community documentation. The results are often quite good, but they're making a new implementation that matches the observed behavior of the original system to the best of their abilities.
Now there are some exceptions. Nuked MD FPGA[0] is a recent example of an FPGA recreation that is a fairly direct translation of the original logic using silicon die analysis. In this case, the logic is basically identical, but as you guessed the physical layout is different. Generally speaking, you write FPGA "gateware" in a language like Verilog or VHDL. These don't intrinsically have any information about the physical layout of the logic which is handled by the toolchain instead. As wmf says, this is generally not a problem most of the time. For synchronous logic, either the total propagation delay is small enough for a single cycle or it isn't. The toolchain will estimate this delay and report whether you met timing or not for the configured clockspeed.
Not everything you can do in silicon translates well to FPGAs (both clock edges is also generally not well supported for instance), but for the most part these things are easy enough to work around.
[0] https://github.com/nukeykt/Nuked-MD-FPGA
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| 1 | Nuked-MD-FPGA | 284 |
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