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The Sizing:Zone, Cooling Minimum Air Flow Fraction input is used in two places as far as I can tell. I doesn't matter which cooling air flow sizing method is used, if this field is entered then it is used here:

DesCoolVolFlowMin = max(DesCoolMinAirFlow,
                                       DesCoolMinAirFlow2,
                                       DesCoolVolFlow * thisTUFZSizing.DesCoolMinAirFlowFrac);

and here:

// set the zone minimum cooling supply air flow rate. This will be used for autosizing VAV terminal unit
// minimum flow rates (comment seems incorrect, really used as a minimum lower limit for the maximum air flow)
FinalZoneSizing(CtrlZoneNum).DesCoolVolFlowMin =
    max(FinalZoneSizing(CtrlZoneNum).DesCoolMinAirFlow,
           FinalZoneSizing(CtrlZoneNum).DesCoolMinAirFlow2,
           FinalZoneSizing(CtrlZoneNum).DesCoolVolFlow * `FinalZoneSizing(CtrlZoneNum).DesCoolMinAirFlowFrac`);

Don't worry too much about what this code does, more importantly that input is used to limit the cooling minimum flow rate during the sizing procedure.