Thanks for the clarification! I checked the spec docs for the MYSX connectors but they didn't mention any fixed pins, just the purpose/pin type. Anyway, for different MCU it will inevitably be different pins. On Arduino Pro Mini since there are only two external interrupts there's no escaping D2, the analog pin on the other hand in an easy fix either use a different pin for battery measurement (A6/A7 is only a via away) or a different pinout on the MYSX.
I couldn't find any instructions for the flash memory, please share a link when you can. Also is it possible to add it without the footprint on the PCB?
PS. I just ordered a set of 10 PCBs through Open Hardware