OptiBPM Designer can display the Z axis on a different scale from the X or Y. Go to View >> Layout Options. The Display ratio panel in the Options dialog box will let you dial any Z to X ratio you want.
The interface suggests the dimensions to be microns. However, the simulator scales everything to whatever was specified to be the optical wavelength in the Simulation Parameters dialog box. Again, the interface suggests to enter this wavelength in microns. However, you could enter the wavelength in nm, cm, m, or even inches, if you like. In that case, all other dimensions would be in whatever units were used for the specification of wavelength. If you specify the wavelength in cubits, the dimensions in the layout will be interpreted as cubits too. 😀