The protractor in your images was made with Conrad Hoffman's software. I believe the files can be printed to a PDF that contains a vector images, so you could edit it in Illustrator or Inkscape. Photoshop is not the best tool for this job – though it has some vector capabilities, too.
When using my site, you could simply enter a different offset angle while keeping the overhang the same.

That way you wouldn't align on the exact null points, but the result would be identical.
Editing a protractor generated by my site is also possible. Instead of printing to PDF, I’d recommend saving the protractor site as a .svg and editing the file in a text editor to remove the html wrapper (just keep everything that is inside the <svg>-tags). That will allow you to open it in Illustrator. But you can change the angle of the grids in the text editor as well. They are grouped, so just search for the first two <g>-tags in the code and edit the value for "rotate".
Alternatively, here are the steps to edit the svg in illustrator: Select a grid, change to the the rotate tool, place a pivot point at the center of the grid, rotate the grid and you're done! Much quicker and cleaner than in PS
Exactly. One would trade intermodulation distortion–caused by the misaligned stylus–for tracking distortion–caused by a misaligned cantilever. Which is the bigger problem? And if they’re both relevant, what would be the best compromise?