Had exactly the same thought about a month ago while setting up a D&D campaign. I had them all representing the same areas as well (except Celestia; I don’t think any single, “mortal” being can truly represent the seventh). It’s an interesting thought though.

This is completely subjective. If you so much as look up ‘chakra meanings’ on Google, you’ll see ten different interpretations on ten different results—the only unified answer among them all is that the Anahata (or ‘Heart’) chakra relates to love.
 
For example, the Vishuddha chakra relates to some as an embodiment of self-expression and communication while to others, it is the embodiment of truth in the spoken word; seeing as how Applejack is the element of Honesty, you don’t think she would possibly represent the throat chakra more appropriately.
 
How about the root chakra, Muladhara? Its inner state is stillness and stability, yet its function is survival and grounding; at the same time, it also relates to the notion of giving energy to the physical body and quelling one’s fears in times of need. Who’s to say that Fluttershy isn’t a good fit here considering the fact that she cares for dozens of animals at her cottage and helps them all to survive, as well as all the times she’s broken out of her proverbial shell to stand up for her friends in the face of her worst insecurities?
 
The crown chakra, Sahasrara—it relates to a great number of aspects, some of which are things like unity and intelligence… and to others, awareness and understanding. At the same time, Twilight (not Celestia) is both a good fit and the completely wrong pony to match this chakra because she knows everything from her books, but she never takes the time to take her nose out of the books.
 
Finally, the sacrum, Swadhisthana—relates to joy, creativity… but at the same time, it also has connotations towards sexuality. And since none of the ponies in the cartoon show any sort of real flirtatious or promiscuous activity, there’s no real fit if you believe this chakra represents best that last aspect. But looking beyond that to the other two (two of many, mind you) meanings of the chakra, you could say that Rarity is the one most appropriate to fill that niche since… well, she’s a fucking designer, a fashionista! She has to be creative, or she’s out of a job!
 
…you see what I mean now, about all this chakra nonsense being completely subjective and up to personal interpretation? There is no ‘perfect fit’, and try all you want to justify it, but there never will be.

I’ve thought about this before, except Pinkie was Third Eye (pinkie sense!), Twi was Crown, Rarity was Sacral, and Spike was throat. Celestia wasn’t in it. I was actually gonna do a series of digital paintings based on it.

Og ponu, booru dev ponu.