We used to fly overlay, manually created LNAV guidance for VOR approaches to airports not in FMS database on the 737 with 2 IRS and no GPS. Not the slightest problem.
Now, Airbus themselves (were made to) claim flying VOR NPA from the box with the underlying NAVAID being U/S is OK, as long as some very relevant precautions are taken.
And at the same time, Airbus prohibits use of NAV for manually created approaches. Que?
The explanation, the very same I believe applies to OP's question, is that the restrictions are operational - i.e. avoiding human error and the training cost - and not technical. Agreed with Check Airman and sonicbum. The idea you can create a waypoint but not allowed to fly them in NAV is completely silly (respecting peculiar applications in the terminal and approach area).