I don't know if this will help, but let me try. I have my limit switches inside my physical limits. And I have my soft limits inside my switch position.
My Y axis has a physical limit of > 625.00mm. I set max limit to 625.00mm. I have minimum limit set to -1.0 and home offset set to -40.00mm. Home is set to 0.00mm. I also have Home_Ignore_Limits set to YES.
I realize I loose a little travel distance doing this, but it seems to work.
HTH
Paul