Some emulators have deficiencies regarding completely emulating RNG calls (which in Gen 3 and 4, resulting in the PID, IVs, Nature, Gender being called in succession, thus with those details, you could reverse search whether the encounter is legal), however as far as I know those details are sufficiently random in Gen 6 and 7.
So all I can say is: Until a sudden new breakthrough regarding successive RNG calls in stats for Gen 6 and 7 is made, the presently known info is that they are sufficiently random, thus even if an emulator cannot 100% replicate it, people cannot tell the difference.
Identification of such mons are subject to change tho, i.e. the sudden breakthrough example I listed at the start.
If you cannot sit in such a grey area, then don't play your games on emu, but do it on retail hardware instead.