Just so were all clear:

>In the distant past... This tower burned in a fire. Three nameless Pokemon perished in it. A rainbow-colored Pokemon descended from the sky and resurrected them... It's a legend that has been passed down by Ecruteak Gym Leaders. Me? I was a trainer way back when. Hohoho!

We dont know the origins behind the legendary beasts. We dont know if Ho-oh revived the nameless pokemon into the new pokemon dubbed the legendary beasts or if they were always the legendary beasts.

We do not know how this event effects how walking wake and raging bolt came to be.

Pokemon Generations is not canon, and the eeveelution theory is fanfiction.