I see your argument, that the AIM allows for the replacement of ground based navaids. Instead of shooting the NDB 29 using the NDB, you shoot the NDB 29, just with the GPS programmed for the same NDB. While I see what you are saying, you are shooting a GPS Approach if you use the GPS! It is no longer a NDB approach (it becomes an overlay approach if that is in the database).
Take a look at AC 90-94. I'll quote some info:
5. OVERLAY APPROACH.
In order to accelerate the availability of nonprecision instrument approach procedures that can be flown using certified GPS equipment, the FAA has authorized the GPS Approach Overlay Program. This program allows pilots to use GPS equipment to fly existing VOR, VOR/DME, NDB, NDB/DME, and RNAV nonprecision instrument approach procedures. The purpose of this program is to permit pilots to transition from ground-based to satellite-based navigation technology for instrument approaches. Approach operations are defined as that phase of flight from the Initial Approach Fix (IAF) to the Missed Approach Point (MAP) when flying an established nonprecision procedure. The approaches to be flown with GPS must be retrieved from the avionics database. (Refer to Section 2, "Airborne Navigation databases" for a more detailed description of the required database.) GPS equipment may be used to fly all codable nonprecision instrument approach procedures, except localizer LOC), localizer directional aid (LDA), and simplified directional facility (SDF) approach procedures. Any required alternate airport should have an approved instrument approach procedure (other than GPS or LORAN-C) which is anticipated to be operational at the estimated time of arrival.
Emphasis added by me. What you are doing by just selecting the NDB goes against the entire procedure of using GPS for an approach. You must have RAIM, you must select approach sensitivity, the entire procedure must be loaded, and the receiver must "arm" before using the GPS as a navigational device. All things that it does automatically if you load the approach contained in the GPS! What you speak of using it for (Direct to XXX) is simply for the enroute environment.
AIM 1-1-21 (f) (5) (a) through (f) allows the replacement of GPS for ground based navaids. HOWEVER, keep reading and under (f) you will find a "Note: This approaval does not alter the conditions and requirements for use of GPS to fky existing non-precision instrument approach procedures as defined in the GPS approach overlay program."
For your safety please read AC 90-94!!!
~wheelsup