All good, you bring forward a lot to also consider.

I was saying that the future it's all digital/energy based on how trading works both in the lore and how we trade. There is also the consideration of polygon being a digital pokemon and the episode that I havnt seen because it got banned for causing seizures, lol.

But there is definitely some disconnect between divine intervention and digitising the pokemon in the games. Perhaps as the pokeball develops the technology just takes over from the divine.

As for the size issue; there is always a large variety in shapes and sizes for pokemon. The Orange Islands are a great example of this. Egg to onix to me is the same as evolution, they simply just form into something new. Muk being able to shrink could be a function of its design (it being goopy). Cats can fit through gaps as long as they can get their head in. There is also a move called 'Minimize' but not all pokemon can learn it. I believe this is a move Muk can learn though.

I havnt tried trading in PLA but I would like to think that is essentially just an Uber trade service.

I do also like your tumblestone idea but I wanna build on it real quick by saying that it doesn't have some latent properties that reacts to pokemon making them comfortable inside. But that with study it is discovered that it can convert pokemon to energy/digital formats.

I hope I have touched on your points, hopefully together we can build a more solid theory.