So today I spent a few hours doing a string wheel alignment. The string showed the rear wheel was misaligned to the right which is what the MP tool was showing. Below are photos of my final swingarm markers. Left is between mark 2 and 3 and right is between 1 and 2.
This matches Seawalls markers, also out by about one marker, also misaligned to the right.
The MP is now aligned even with the longer pointer. What I did notice is that to the eye the MP was about aligned but the string alignment was still not spot on.