A friend of mine who was into Mazda wankels for years has this perspective:

Given the torque characteristics and a market segment perceived as more performance-oriented, the engineers probably decided on relatively lower gearing for the manual transmissions to minimize the need and delay of downshifting (for hills or passing) at highway speeds.

The automatics have less need for lower gearing due to their relatively instantaneous and precise computer-controlled downshifts, and a market segment perceived as being less performance-oriented and more comfort/convenience-oriented. So, they were geared much higher (with side benefits of better highway fuel consumption and less engine noise).