Continued from above:

3) Next, I decided to test the dome positioning at two positions that I think simplify the issues. I first put the scope on the East side of the mount dead flat, looking due north (see figure and picture). I believe this will remove any issues of offsets in pier position in the N-S direction. Thus, the only measurement problems I can have are E-W offsets, Up-Down offsets, and OTA length offsets.

In this position, the spreadsheet says the dome should be at 0.2°, INDI places the dome should be at 10°, and I estimate the dome actually needs to be at about 16° to be centered. About 1/2 of my scope view is occluded by the dome in this position.

The software settings are shown in the attached image. Sorry for the crazy moire patterns.