I'm not sure I understand. When I draw a line a 1 pixel width are you saying it does not translate to 1 pixel of the resolution? I would think that 2048x1536 would produce more PPI, thus details, than 1024x768, giving more and smaller pixels within the same physically measured dimensions of a canvas, eg 5"x3" or whatever arbitrary size. So the ipad's PPI would increase from 132 to 264 if the screen size stayed the same.
The screen can have 2048 x 1536 resolution, however the input (touch sensor) that covers the screen, does not have anything near this same resolution. So my guess is that a drawing program (at native resolution) is limited to the resolution of the input / touch sensor.
I've seen DPI and PPI confused, and interchanged before. From an image standpoint, they can be interchanged, however I've seen DPI relating to scanner input resolution, and printer output resolution - whereas PPI is the resolution density of your LCD itself.