Mass production is pretty specific discipline and each manufacturer has different preferences. So you either know it or you better talk to them first. Also it's mass production (500 pieces) and pass production (500,000 pieces). Typically there is some test-jig in the end of assembly line which does both FW/diversified data flashing (to all MCUs which require it) and testing (some basic things like DTM - if you run BLE stack in your product - etc.)
If you are asking for flashing then some people use off the shelf SEGGER J-Link/J-Flash tools, some prefer custom made or 3rd party bu more specialized tools. There are many of them presented in Nordic blog zone and this Infocenter page.
Finally if your beacon is based on nRF51 or 52 chips then yes, it should be easy to make these fields configurable in the FW and set them during FW flashing in production.
