It's very simple, it's the preponderance of evidence.
Sure, if one Pokemon did it, like Darkrai, apply it only to him.
But, when we systematically see several people, unrelated to the feat in question perform, the pattern is simple.
Do we now take it that we need to see every Arboreal Monkey to know they can climb trees? Of course we don't, we see that the pattern is repeated, that they, not as individuals, but as a species can do these actions.
If you don't like that analogy for arbitrary reasons, we only see around a few thousand people in our lifetime, maybe more if you're particularly popular, yet we know that there's well over 7 Billion other people on Earth, do we now only apply the status of "Existing" to those we've seen, and those we haven't see exist as figments of imagination? Demanding proof that the others have to prove their own existence? Obviously not, that would be absurd.
Like I said in my previous post, it isn't as if these Pokemon have some special connection to Space-Time or some special ability that would let them do this, in fact, it couldn't be more obvious that it's the everyday Pokemon like Shedninja, Ninjask, Piplup and so on who are common Pokemon, not some rare or legendary Pokemon with remarkable powers.
The opposition seem very sure in their opinion, since evidence is given, it's their turn to provide their evidence disproving the claims presented.
