Wow!
Well done, and very well explained! Although I don't quite yet understand it, but that's not your fault!
I have one question / bug report (maybe). I just had a look at the color VGA example. I haven't connected anything to an Arduino yet, just looked at it in the IDE. It compiles just fine (and at 1116 bytes!)
Of course from you screen photo and all it seems to work, but did you do some trick with this part (line 96-97)?
const byte verticalBackPorchLines = 35; // includes sync pulse?
const byte verticalFrontPorchLines = 525 - verticalBackPorchLines;
It would seem that the byte "verticalFrontPorchLines" is truncated or wrapped around?