Cary,
If your reference standard (least disturbed ecosystem) for the soils / wetlands in your geographic area (reference domain) is 4 cm of O horizon, than that sets the 1.0 score for your functional model. It would not be HGM appropriate to set the 1.0 scale for a Histosol or Histic Epipedon if that is not appropriate for the wetlands being sampled. I concur with Craig that thickness of organic layer is more appropriate in a biogeochemical functional model. For water infiltration I prefer to use soil properties that reflect infiltration / conductivity rates such as bulk density, crusting, or morphological indicators of soil physical quality (i.e. structure, rupture resistance, micro-pores, etc.).