Great measurement tutorial, thanks so much @gdon_2003. The software history helps explain a bit too.
Measuring distances I’m getting (roughly) X=447mm and Y=451mm. I pulled back from the mechanical stops a bit. This explains why the Rapid Position movements is sending the machine past the X limits: loading the defaults for the 4 XL sets the X travel dimension to 865mm! Which turns out to be correct… I actually have a 4 Standard and I somehow got stuck thinking it was the XL. Brilliant.
Setting defaults for the 4 Standard sets travel dimensions X=445 and Y=455. Much more sane values. Thanks for helping me through this one.