The Legendary Beasts myth was always a mess because Entei's Silver dex entry say that they are born when a new volcano emerges. This dex entry implies that there are more than one Entei and they needed a hypothesis for their origin.
That’s one way of reading it, and probably the more straightforward way at that. But to illustrate an example, if you were to think of it from the perspective of people in-universe, even if there were definitively only one Entei in existence, it wouldn’t be telepathically AirDropping its lore to everyone nearby as it roamed around. Someone who isn’t aware of Ecruteak’s history could happen to see Entei in the wild and then go on to develop their own mythology around it, and that could be how you get the volcano association.
(Now that I think about it, I feel like that’s kind of an interesting untapped conceptual well — Legendary Pokémon from one region who have also developed a separate role and mythology in a different region. Like I
guess you sort of get that with the Galarian Birds and Regis in the Crown Tundra, but they were all actually pretty irrelevant to Galarian mythology, all things considered. Especially with the Regis, where it seems to always be essentially the same thing, every time, no matter what region they appear in: “Mysterious titans that were sealed away in what are now old ruins.”)
Was it ever explained in Gold/ Silver why the trio are found dormant in the Burned Tower? When I played as kid, my interpretation was that they died in the fire, Ho-oh resurrected them but left the beasts there dormant to be found by the player much later, which led me to think that Ho-oh was a dick.
There’s an NPC who says this (in both the originals and the remakes):
“Ecruteak was also home to three Pokémon that raced around the town. They were said to have been born of water, lightning, and fire. But they could not contain their excessive power. So they say the three ran like the wind off into the grassland.”
HGSS add a little more detail from another NPC:
“When this tower burned in a fire, three nameless Pokémon perished in it. Then, a rainbow-hued Pokémon descended from the sky and somehow brought them back... The people were afraid of power such as the rainbow-hued Pokémon had shown. They tried to control it by force. The nameless Pokémon made no attempt to fight back. Instead, their great sorrow compelled them to leave.”
From that, I gather that they were perfectly able to roam around, but for some reason must have come back to the tower to rest roughly sometime around the Gen 2 protagonist’s journey.
(and themselves if you think of things like the Zoroark movie where separate specimens exist for the Shiny trio).
When you think about it it’s all kind of a moot point anyway since Pokémon takes place in a multiverse in which time travel and trans-universal travel are possible. But frankly even before Gen 6+ made that explicit, I tended to be of the opinion that the very existence of Shinies for Legendary and Mythical Pokémon indicated that
none of them were truly unique specimens. But then you get into a sort of debate about where the line is between things that are just there for gameplay consistency versus things that are meant to be part of “the world.”
And naturally, each medium is going to have its own canon. Hypothetically, the anime could say there are multiple Legendary Beasts while the games could say there’s just the one set originating from the Burned Tower, or vice versa. (Not that the games ever actually
did say that, but certainly a lot of people felt that it was implied. See also the Lugia/Legendary Birds connection that was explicit in the anime but has only ever been lightly gestured at in the games
because of the anime.)
This would also keep consistent at present/hindsight with the imagined "Triple Beast" in the Scarlet Book (predating the Burned Tower incident by 50 years and in a completely different region of the World from Johto), being another Paradox based on existing mons but warped rather than a 100% fabricated idea.
Honestly this was never even really an issue given the time travel of it all. The time machine isn’t built until roughly the present day and is the whole reason why Wake, Fire, and Bolt are in Paldea, so there always had to be some sort of temporal weirdness behind Heath’s team being able to observe those creatures, and the DLC implies that it was Terapagos bridging the two eras like it does with the professor at the Crystal Pool. So even if someone were a staunch diehard about subscribing to the idea that Raikou, Entei, and Suicune didn’t exist at all until the Burned Tower incident, the apparitions of their Paradox counterparts in Area Zero still wouldn’t contradict anything. At worst it’s just a good old bootstrap paradox, which is a concept that Pokémon has dabbled in before.
