While not a part of the upcoming release (version 7.0.0), we have tentatively scheduled this feature for the next feature release (e.g. 7.1.0). It would be a check box on the window that appears when you use the "File"/"Ladder/Misc. preferences..." menu. When checked, all brackets that have 2 wrestlers would be best 2 out of 3.
Since we are busy working on version 7.0.0, I cannot estimate when the subsequent version will be available