Just to confirm that you do not build anything off the runway extension point.
The 3.1 Nm Runway extension is merely to define the track emanting from the runway.
Once the new point is created at 3.0 Nm (on the defined track from the runway) then the Runway Extension at 3.1 is deleted/overwritten.
Then the new user defined point (3.0Nm) can then be 'built' off.
Our mob tends to frown on them as well but knowing how to manipulate the FMC is valuable.
Let me know if you have problems as I can send you a couple of screen shots.