Not quite. Almost all NES emulators just emulate the inputs and outputs of the chips involved, they don't actually model the chip layout exactly. That's a limitation of emulating hardware in software for the most part. Without perfectly implementing the chips involved with all their associated timing and clocks there's no guarantee that some behavior might be slightly different.

When emulating software in software, it's much easier to confirm that the exact same operations are done, and you can in some cases fully verify the solution.