I read your description of your e-stop, etc, wiring with interest. Always good to see someone else's approach. Couple of questions come to mind.

Did you consider use of a safety relay? I managed to pick up one cheap on eBay, partly because it lets me switch a number of circuits from the e-stop switch, convenient way to configure "momentary contact" standby switch, etc. Does your e-stop connect to a latching relay or similar?

You mention limit switch triggering as equivalent to e-stop. I can see why you might want to do this, but will it give problems in separating limit and home switch operation? I use drive fault from my digital drives to trigger e-stop but limit/home switches go direct to CSMIO (similar argument to yours re dedicated firmware - no PC involvement).