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Are we talking following the game's rules or just assumptions? Because at this point there's a theory that says that Genesect is a robotic Kabutops. Or that Entei, Raikou and Suicune are hyper versions of Flareon, Jolteon and Vaporeon.
Also, pokédex entries sometimes even contradict themselves in different games, just sayin'.
But the dex entries are Canon. You can't argue with canon facts even if it contradicts itself. Sometimes it could just be that it's contradictory because you aren't able to see the full picture yet. This is where fan-theories begin to crop up. But in all honesty, if it is deliberately stated in the games, it is true unless retconned. Thus, Entei, Raikou and Suicune could indeed be hyper versios of the orginal Eevee trio, unless retconned. Arcanine to this day is still labeled as a legendary pokemon in the dex, and Entei's dex entry is still cited as recently as Gen4 in SoulSilver, so imo, I'd say it holds true. Legendary Pokemon are not as rare as people want them to be. There are multiple versions of the same Legendary Roaming around, barring maybe Arceus, since it's the creator Pokemon.
And interesting theory also, is that Ditto are failed Mew clones, and that Mew is the Origin of all the Pokemon. Both make sense and are nice food-for-thought.