Yes M502 does respond with"Hard coded Default Settings Loaded"

When I use the x and y home buttons I can confirm with an M114 that it is in fact at X0 Y0.

Also the numbers are not thrown off after a G28. G1 F1500 X0 Y0 will bring the hotend back to the correct X0 Y0. It isn't until I run the G29 that things get thrown off.