Preparing environment for production department

Knowing how production environments are always hard pressed for time, I wouldn't do it. Instead I'd leave some pads on the bottom of the board to get direct access to the serial eeprom. I'd guess you'd want a pin jig of some sort to automatically test the boards anyway. Then during test, you can load the serial eeprom with whatever sof you want reliably and quickly. The other way takes a fair bit more time, and has more links in the chain to go wrong. The extra board cost of a pad layout is small, and generally the real-estate cost should make up for the testability you gain.