Jon from Splitwise here, thanks @mjmahone17 for mentioning our answer to this problem.
I think if you have complex or specific preferences about rent splitting (ie I don't want to live next to the kitchen) and live with a bunch of fellow nerds, an implicit fair division system may work well. The NYT calc is a great new implementation the Francis Su paper - the old Java one was broken.
If you have non-nerd roommates, couples living together, or are already assigned to rooms by fate or immutable preference, that's what the Splitwise calculator is for. The price are based on square-footage, survey data, and common sense. Not everyone is willing to change from the room they like, or sit for an auction.
Good point, for cases where you can't actually make a choice a curated price calculator is the best one can really hope for. In any case splitwise is a nice product btw :)