[It's all just text, but please know that Leonardo read this entire post with equally great enthusiasm.]
Perhaps there is a way to measure the energy that is released upon the egg hatching? Or it could be some unknown aspect of their reproductive system that causes these eggs to... well, act as you suggest they do. After all, if these pokemon can shrink in size to fit inside a rather tiny ball, then perhaps their size is somewhat easy to change depending on how much energy they have at the moment? And perhaps levelling up, as the index calls it, allows the pokemon to access greater stores of this energy.
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Perhaps there is a way to measure the energy that is released upon the egg hatching? Or it could be some unknown aspect of their reproductive system that causes these eggs to... well, act as you suggest they do. After all, if these pokemon can shrink in size to fit inside a rather tiny ball, then perhaps their size is somewhat easy to change depending on how much energy they have at the moment? And perhaps levelling up, as the index calls it, allows the pokemon to access greater stores of this energy.