Yeah, only having a few actors means very little if they're good enough.
Just look at how many Simpsons characters are voiced by Hank Azaria, Harry Shearer, and Dan Castellaneta.

I do agree, though, that Luna's quieter moments do sound a bit like Rarity.

I don't think they'll ever have an episode with both Rarity and Luna.

haha, it's not like a Seth Macfarlane cartoon when they don't care that two, three, or four of the characters have the same voice actor with only a slightly different inflection.