Actually, 2 or more Pokémon that have the same IDs are not necessarily clones... you could catch more than one of the same Pokémon with the same PID pretty easily by abusing the RNG on a non-legendary Pokémon.
Are you sure about that? Because I don't RNG abuse, I Pokésav, but from my Pokésav I can see that:
A Modest Male (Class 1) Probopass can have PIDs...
1768256240
3979748340
3609510640
2382487540
371387390
964874740
2816746490
1845625840
4009113340
751368690 ...so on and so forth.
3979748340
3609510640
2382487540
371387390
964874740
2816746490
1845625840
4009113340
751368690 ...so on and so forth.
Any given Spinda can have one of 8,589,934,592 (including shiny and not shiny) patterns, however, you can only catch 524,288 of the shiny Spindas in each game save, because it is partially based on your TID and SID. The rest of what the Spinda looks like is determined by the SID, so if you were to catch a shiny Spinda, there would be over five hundred thousand different ones you could catch before you would find two identical ones. I use Spindas in this example because every Pokémon can have a huge amount of PIDs, but Spindas actually show their PID in a way.
you could catch more than one of the same Pokémon with the same PID pretty easily by abusing the RNG
If by this you mean intentionally catching one with a specific PID, then okay, I understand, if that isn't the case, then I find it extremely unlikely