There's a difference between rarity and value. A pony that has a ton of individual pieces out there (like G4 fashion style applejack) can be super expensive because there's only so many on the market at any one time and/or they're very sought after. Laws of supply and demand, really. That's why some people say that some rare ponies are $50 and others list rares as being $1000+.
I think rarity really means that there's not many out there in the world, such as the Takara ponies, certain nirvanas (Italian big brothers) and factory errors. But how many people want to buy a G4 pony with an eye printed badly? It's "rare" in that there's no pony exactly like it, but the value is pretty low, so most people wouldn't bother with it.
The rarest G4 out there (since it's the gen I know most about) would be pink wave 1 Twilight blind bag. They only made her with the first "set" of toys in Europe, so she was quickly replaced with the purple toy. Most people don't realize she's so rare, so her value isn't super high.