I wouldn't worry unless you're using open loop steppers...
Your limit switches are coarse switches which stop the travel before the machine hits the hard stops like you said.
Your home switch should only need to be used for each initial power up. A .005" difference between power ups on a machine you are hoping to run production (I'm assuming here) and the associated diameter compensation isn't something I would be particularly worried about. Depending on your tool holding it might be as simple as adjusting the X value on your G54 to compensate all the tools for the new home position. This would be no more difficult than setting a tool on a conventional DRO.
This is all assuming you're using something more advanced than open loop steppers.