>>54467408The thing that made the original story special was Ho-Oh giving the trio a blessing they didn't ask for, saving their lives but also changing them forever, making them be feared and chased forever.
The change was an involutary application of power onto ordinary beings, a risky move that saved them. I'm in no way advocate of the Eeveelution theory, that's also not the point: It doesn't matter what the Legendary Beasts' original appearance was like and what pokemon they were, what matters is that they were ordinary pokemon turned into legendaries through circumstances beyond their control and now feared for their powers.
If they were already legendaries or mega-powerful pokemon before their deaths, then the story loses meaning and also makes no sense in-universe, because remember, strong and unruly pokemon were shunned by humans before the invention of the pokeball but the trio lived among humans before the tower burned down, and since the Paradox Mons are not ordinary pokemon it makes no sense for them to be living there.