I figured this out, in case anyone is having a similar problem.
Strangely, when using the MIDI learn button inside of MidiDesigner, the control was not applying the correct MIDI message. Inside of my Softstep Editor, I had the physical pedal programmed to send CC 60 on channel 1. When I was using the "learn" button, it was not applying 1-60 to the footpedal supercontrol; rather, the message was listed as 1-47. When I manually changed the CC message of the supercontrol, it began to respond appropriately.
I'm not sure if this is a bug, or something I'm still not clearly understanding about the MIDI learn feature.