No flight planning program can be relied on for obstacle clearance - unless you are flying at airway MEAs.
Flitestar (which I am familiar with) should not be used that way either, despite showing a pretty picture of the profile.
I think Navbox does offer some sort of notam briefing which comes from a connection to Avbrief. I have not used this since the early days, when it wasn't working.
Not sure what you mean about incompatible coordinates in Flitestar?