>>vetrom+Fc
I've worked with automated EEPROM/Flash programmers (earlier versions of this line:
https://www.bpmmicro.com/device-programmers/automated-progra...), and used pre-programming services from distributors, like Digi-Key, but that was the exception. It's almost exclusively faster, cheaper, and easier to load firmware from a test fixture. You need to test the assembly anyway, and it's much easier to update a test procedure, when a new firmware is developed, than to update and track inventory of pre-programmed devices, especially when different firmware versions are needed for different hardware variations.
Pogo pins are only really needed for mass production, especially for reducing repetitive stress injuries. For one-off updates, if a header isn't populated, it's easy to hold an unsoldered header in place, for long enough to flash an update.