I am not sure what the right answer may be but my guess is this.
OKW was the first
DVC resort. At the time Disney wrote up the contracts and determined the points, they figured low for a 3-br villa. Boardwalk and Saratoga are the only resorts that have 3-br villas. I think Disney figured that 3-br were more valuable at the time they designed those contracts; therefore, costing more points. Plus, you gotta figure location too.