First of all, sorry for the late answer.
I think your method's weakest point is the alignment, just like in my case.
"Select two points along the robot base's X axis and measure them with the tracker. This will generate two non-parallel lines. [...] Repeating this process for points along the Y and Z axes of the robot base would allow one to find all three relative rotations [...]"
The three vectors will not orthogonal, because the angles between the vectors are not exactly 90°. I don't know how will it affect to the measurement accuracy.
Another perception, your base calibration method depends on the robot's dynamic parameters, like the bending. So when you move the TCP to the known locations, the controller already will show a false position and the fitting will give a bad result. But I don't know how bad is it, maybe the error is negligible.
Must try it out and compare the results of mine base calibration method and yours. Sounds easy, but how to compare? How could I know, which result is the better? Well, it's a hard task