I have a theory..
What are your opinions of the basic principals..in the theory of particle science. Being applied to pokémon, by the means of how they are capture and contain creatures?
Since, to be able to contain a living object in a small item. They have to particularize the being in a such away, to pull and part then repair the DNA of said subject. By the energy beam, at which is initialized from the pokéball, opening on the object or manually being opened, to activate the beam.
That beam probably, being what causes their DNA to particularize and then be transfered to a small object and restored, to it's original condition. If I'm not mistaken, that is the basic concept..behind particle science. Which as far as I can tell..we in this world, are not quite up to that technological level, to even be able to think about doing something like that.
Something that has been said that we could never do, just from the share fact, your tampering with the genetic code..by means of pulling it apart and restoring it to it's original condition. Which on that fact, it seems the world of pokémon has mastered this ability, since, they can both dismantle and restore a being both ways. From an average size object to shrinking it, then repairing it to it's original form.
Perhaps in some essence, there is also molecule transference there..as well.