A legend is first and foremost a LEGEND AKA "An unverified story handed down from earlier times, especially one popularly believed to be historical."
In other words, nothing say that the 3 beasts were resurrected or anything as such. We don't quite know what role Ho-oh has in the world. He he often called the "guardian of the skies". What if Ho-oh had the task of protecting the skies. Task given by some other legendary pokemon... Maybe he did his task but one day, he and Lugia decided that they needed to something to be the guardians of the land. Thus, maybe they created these 3 together. After all, what is between the skies and the seas? The earth. Someone may have witnessed the act and thought that Ho-oh resurrected some pokemons when in truth, these 3 were created from the knowledge and wisdom of Ho-oh (and possibly lugia).
I do think it could also be eevee too. Maybe eevees were not always rare. Maybe they occupied the tower when the even occured. Since eevees are mutants, when ho-oh ressurected them, they still had the power of the storm, water and flame that killed them. This mixture of power transformed them into the legendary beasts we now know instead of simply being flareon+jolteon+vaporeon.
So yeah... unless a pokemon game make us re-witness said events, we will might never know :-/.