I'm gonna say wheel dish is too far to the NDS. Maybe because the spokes are too short to put it in the right spot. Looking at the first picture, the left brake pad sits closer to the rim surface compared to the right pad, in addition to the rim being closer to the NDS chainstay. You've already confirmed that the dropouts are centered.
Take it all with a grain of salt. An easy check for wheel dish is to put the wheel in backwards, and see if the rim ends up closer to the DS chainstay. With what looks like 3 to 4 threads visible on the NDS spokes, I would measure all the necessary parameters and find the recommended spoke length to order replacements.
An interesting thought... What if the DS and NDS spokes were inadvertently swapped when the wheel was built? If you have a lot of spoke past the back of the nipple on the DS, that might be the answer.