They can both be equally authentic, there's nothing preventing either from doing the exact same thing as the other. But the software based one will have a lot m

They can both be equally authentic, there's nothing preventing either from doing the exact same thing as the other. But the software based one will have a lot more overhead keeping track of cycles and making sure things interact at the right time. As willis936 points out, decapping can let us see the exact logic a chip uses, but only a minority of chips are decapped. It's extremely expensive and analysis is time-consuming. Most stuff is reverse-engineered. That doesn't mean it's all HLE, we can infer a lot of behavior, and the composite timing is known, so it's close enough to use, but not to archive the design for future generations.