OK, let's make the question a bit more accurate:
"Why must the limit switch known by Mach be a last chance safety system?"
I would say you should be asking if it is possible to set soft limits to act via a physical switch. This is possibly where things are getting confused, when talking about limits we normally think of Hard Limits and these should never rely on software to control them, software as well as the hardware is ok but both must work independently.
What you are wanting is soft limits which are activated by physical switches which can be moved if required.
That is not possible with Mach as is and would be a good feature to have for some BUT it should never be used instead of Hard Limits, they should always be present.
How easy it would be to do it in the code I have no idea and only Brian could answer that, I suggest you contact him now and ask for that feature to be added into Rev4 as it will likely be easier to add it now rather than after Rev4 comes out.
But please do not ask for Hard Limits to be turned into Soft Limits

Hood