The centre of that PAPI beam (ie half way between angle C and angle B) is not parallel with centre of the ILS GS. Angle C is parallel with the GS; that diagram indicates that that PAPI is set at 2.75°. They are neither coincident in angle or GPI.
You are missing the numerous factors involved in the design. There are differences in the assumed eye height vs the antennae height. (Note the EW eye to wheel height vs AW antennae to wheel height factor)
This is from the design manual, so as you can see, there are many factors involved.
EDIT: A squared...I never said it had anything to with the incident, I said it brought the issue of multiple TCH and GPA's to the forefront.