I was a bit confused by your details, after reading a few times, I think I understand what you are trying to do. You are using a custom board, not NXP EVB, and it has 2 flash memory devices connected via QSPI. Your board is also setup to use the Serial RCON, which means the configuration comes from the value programmed to EEPROM (as is an option with the NXP EVB). We already have a script for this to change the value, probably you already know of this:
HOWTO: Program Serial RCON using S32 Debug Probe S32G2xx
I suppose since it requires having S32 Debug Probe connected to the board via JTAG, and you noted that you need some option aside from debugger, that this is the issue you are faced with?
Unfortunately, we do not have a solution outside of this method. I will check if our developers could consider if there would be any other way to accomplish this.
What is the reason you are unable to use the Debugger/JTAG method?