I was digging through the Step Sequencer code and noticed that if you changed one line of code I think it could (kinda) handle quarter / half / third octave transposition.
Current:
const int32 AdditionalOctaveNotes = (int32)*AdditionalOctavesInPin * 12;
Modified:
const int32 AdditionalOctaveNotes = (int32)(*AdditionalOctavesInPin * 12.0f);
(Line 590 of StepSequencePlayerNode.cpp in the Harmonix source directory)