The biggest reason for suggesting to follow the RAMPS connector pin out is it is a very standard board. But if you are going to supply the Pins.h file for your board, it really doesn't matter how you bring things out.
I would suggest you make sure all of your end stops an Z-Probe connectors are on pins that can generate a processor interrupt. That helps with the end stop detection. (Incidently, the RAMPS board has all of its end stop connectors on pins that can generate interrupts.)
I would suggest you make sure all of your end stops an Z-Probe connectors are on pins that can generate a processor interrupt. That helps with the end stop detection. (Incidently, the RAMPS board has all of its end stop connectors on pins that can generate interrupts.)