I've seen, quite often actually, a circuit that will have an eeprom or flash chip soldered next to the application chip. Take a look at the ESP8266, it has some kind of programmable memory that sets up the SoC.
My question is how was that eeprom/flash chip programmed if there aren't any programming ports on the application board? Is there like some pogo-pin programmer used during assembly or a socket that they drop each and every one in before soldering? Those options seem incredibly time consuming.