I think I know why you might think disobedience worked that way, and I'm not sure if it applies to you, but in Gen III both Mew and Deoxys (maybe also the other Mythicals?) disobeyed you always if they didn't have the fateful encounter flag.
I actually feel the opposite, dude. By the having the expansions be digital the people that bought early could upgrade. Compare with the third versions, where if you bought early you were screwed because no way to update beside buying the same game again.
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