+1 I also prefer to see chords this way with low E string as you have it.I actually like the chart, but not in it's current orientation. I think it helps see the relationship of the notes on the fretboard.
OP - the chart (for a right handed guitarist) should look more like this
That way, like someone mentioned, the chart looks more like the fretboard as you are looking down at it from a playing position. Easier to visualize that way. Noone was mocking you, just having some fun. I don't quite understand your original question either. I think you are asking about the relationship of different notes to different scales. Everything scale has a root note and climbs from there, but each scale has a different pattern of notes....sharing some notes and not sharing others. Good luck in your process.