The same thing happened to me, I was passing without thinking about it, I was a while on Route 01 after killing a Dark Arceus, out of rage, I spent a long time looking for it, and it appeared after ~30 min I think, the normal, then I went without thinking, to 'Fungal Cavern', where in less than 1 hour approx. I found Mewtwo, Lugia and Kyogre (out of nowhere), and well, curious thinking I was lucky I stayed a while longer there and I did not see them again.
What you say is true, I'm returning from time to play this to kill time and I'm seeing it more interactive part of walking, before it was a headache, so I left it.
I hope to find the others, but I don't know much about it, so it's just a hobby. Greetings :v
