What about Entei's Pokedex entry? An Entei is born every time a new volcano appears.
This would lead me to believe that there's at least more than one Entei.
And if Jolteon, Vaporeon, and Flareon were revived, why not any of the other Eeveelutions?
I'm not sure how accurate the Pokedex entries are. A lot of them say things that contradict what we know the Pokemon can do. Also Looking at the Silver entry it says, "A Pokémon that races across the land. It is said that one is born every time a new volcano appears." Having it worded as "it is said" makes it sound more like legend than fact, but who knows. I'm pretty sure there have been multiple Enteis in the anime, but I'm unclear if the anime acknowledges that they have encountered multiple ones.
As to your second point, in the games it is stated only three Pokemon perished in the fire. Entei represents the flames that burned the tower, Raikou represents the lightning that struck the tower, and Suicune represents the rain that ended the fire.