Very good you're trying to analize this stuff dehowe85 i think this is the way to remember the fretboard and the scales.
You can see very clearly that there are many different ways of looking to this. For me the D shape is the 5th position which is played (When playing in D) on the first 4 frets. I understand your way of looking to it but bare in mind that when you play G maj the D shape is not the first shape anymore. In the end it doesnt matter wich position is which position (thats what i tried to say in my previous answer) a scale is a sequence of tones D-E-F#-G#-A-B-C#-D and if you play them right in this order it doesnt matter how you play them. Therefore it is importante to remember the fretboard and the scales with their formulae.
The main rule with the CAGED system is that you play a scale with your 4 fingers all dedicated to one fret with some exceptions, those exceptions are stredges with your finger 1 or 4.
This is my point of view, im not saying this is the RIGHT one.