How to preset an I2C IO expander
You already indicated that you have a microcontroller on the board with all the I/O expanders. You said it already talks to the I2C stuff already!! Why not just have that microcontroller firmware setup the needed default initialized state of the I/O expanders. 

If you needed several different ones of these initialized states you could even add several jumpers into that MCU to select the particular profile that is needed.