Tools required to burn code in a quad flat microcontroller
Either add an in-system programming interface (e.g. header pins, or some kind of pad for a programming jig),
OR get the manufacturer of the device to factory program the devices before they're installed in the circuit. This is a service which is typically offered by the manufacturers - they must have some kind of test / programming rig in the factory, but they would probably need that anyway because I am guessing that most microcontrollers, even re-flashable ones, need some one-time programming (e.g. maybe calibration data or serial numbers etc) anyway.
I've been making very small volumes, so I have an in-circuit programming connector on my boards, and I manually program them