HIFLYR

I have not NavData coded in a while but in the past and pretty sure now the VNAV path as coded in the Nav database will be raised to clear any step downs between the FAF and 50' crossing height for the selected approach. Speaking only for our airline you never have to check crossing altitudes inside the FAF using VNAV i.e. the calculated angle encoded in the Navdata base, only prior to the FAF. Also, you are really only guaranteed terrain clearance to minimums, the final segment is a visual maneuver on a non precision approach. In many FMS there can be only one approach of a given type i.e. only one VOR approach etc. a given runway. There may be a VOR DME, VOR or VOR/A also but only one in the FMS, the standard was to include the one with the lowest minimums. However with most NavData providers you have the option for tailoring the data to remove one and add another or you can backwards engineer another one if required.

I just checked with a old friend who still codes FMS Navdata and ARINC 424-19 spec is to go from 50' above the runway to the FAF and make the VNAV angle clear any step downs between the FAF and the 50' crossing height.