I love the Eeveelutions-to-Gerbils theory.
Now, I find it very unlikely that Ho-Oh created new species by reviving the creatures, formerly Eevees or not. We know that in most continuities there are Gerbils other than the Tower Trio: sets roaming in the games, the Crown City trio in the anime, the Raikou in the Legend of Thunder special which was roaming before the 3-years period where the "player character" would have unsealed them from the ruins, the Entei in Movie 3, etc.
I find it more likely that if (big if) Ho-Oh did revive three creatures and they were turned into Gerbils as a result, either he merely used the Gerbils as a template to perform the revivification, or the transformation was something outside of Ho-Oh's reach (otherwise for a Pokémon known to revive others, we would have heard of other transformations in the events that describe Ho-Oh's powers).
Disclaimer: I did write a fic where my interpretation of Ho-Oh speaks of what he might have done, but he's smart to not commit to any version of the story.
Also disclaimer: Cats Dogs Beasts Gerbils forever!