Hey Craig,
if you want to move in machine coordinates, you got to prepend G53 (Move in machine coordinates). Unlike G54 –G59.2, it is not a modal command and need to be specified on every line where you want it to be applied to the subsequent motion command.
E.g. if you have your workpiece zero coordinate somewhere, with G53 G0 X0 Y0 Z0 you still move the gantries to their machine home positions. No offsets currently active will be changed.
Be aware that G53 only works in G90 (Set Absolute Distance Mode). Note that G53 will fail silently if G91 (Set Incremental Distance Mode) is active (this is a bug). So as a workaround it is good to specify G90 prepended to any G53 command. G90 however is modal and will remain active from then on.