I have to disagree with Thunderforge's interpretation of the Generations plot summary:
Ho-Oh used its mystical powers to revive the perished Pokémon into Raikou, Entei and Suicune.
In my opinion, saying that these Pokémon were revived "into" these Pokémon implies that they weren’t originally these 3 Pokémon before they were revived. I also believe that this backs up why the silhouettes that appeared didn’t resemble any Pokémon that have been seen before. If they were transformed into these Pokémon when they were revived, it would definitely explain why nobody recognized the silhouettes.
What’s more reliable than Generations are the video games. One of the most crucial links between the Eeveelutions and the legendary beasts in the games is their Hidden Abilities. Raikou has Volt Absorb, Entei has Flash Fire, and Suicune has Water Absorb. Those are the exact abilities of Jolteon, Flareon, and vaporeon. The Kimono Girls that worship Ho-oh also use the Eeveelutions.
This is just my stab here from what I’ve looked into from other sources. I’m not stating that this is fact since Game Freak hasn’t confirmed anything, I just believe there’s enough information to back it up and that I don’t believe it’s been debunked.