Would it be possible to get an SD image that has the overlay filesystem enabled? This would take some doing in the code, because you would require the files and some settings on machine setup to reside on a USB drive (they could not be stored on the SD). I have been in projects that deployed large volumes of Raspberry Pis and many of the comments in the forum/facebook pages about unpredictable behavior will occur in signficant but small fractions of your user base. It sends a shiver through me when I read them, because I have had similar issues and it is a customer support nightmare to troubleshoot.
Please consider going to the overlay filesystem on the pi in future versions. Overview | Read-Only Raspberry Pi | Adafruit Learning System