There isn't enough met data stored in the PKM to indicate the exact encounter you obtained it from. All it has is the met level, and the moveset really.
It finds a possible encounter, checks the moveset being possible, then settles. If an egg could have originated it, or a wild slot, or a starter, what's to say it is one vs the other? An egg will more often be legal, as it is more permissive with levels AND moveset (egg moves, inheritance) compared to other encounters, hence why it is evaluated first (successfully).
As for PID correlations, those are only a thing for generations where the correlations exist. For VC transfers, the game generates a random PID and EC, and Nature is based on the experience value it is transferred with (modulo 25).