Take an Arduino or Teensy prototype to Mass production - Loading software onto microcontroller
Arduino code and AVR code is essentially the same, at least once compiled it is. The only real difference is the existence of the bootloader, and that is not essential.

For quantities of a hundred or so it is probably most cost effective to manually program them via an ISP connector to the board. For larger quantities Atmel provide a mass programming service to pre-program the chips, but that costs money so the more you have done at once the cheaper it is per chip. I am not sure on Atmel's procedure off hand but others I have used just take either a .elf or .hex file which the Arduino IDE is perfectly capable of producing.

Either way you should design in an ISP connector on your board so the firmware can be upgraded in the future if needed.