You can also define your own board in the boards.txt file. You also need to fill out the fuse settings according to your configuration. If you're okay with not fully exact timing, then you can use the internal RC oscillator to run the Arduino. It also runs at 8MHz so if you want to run at 16 Mhz, you will need an external crystal.
Regarding production programming, if its for 100, you can still program them by hand using a cheap ICSP programmer like the USBASP. They are quite fast. If you want full production or if you are doing batches of 100 and its taking too long to program, then you can get a batch IC programmer or a socketed programmer and pre-program the chips. But for production, since you will still need to do production test on your test rig, manufacturers usually program the IC while on the test rig and with the test program. That way, you add the bootloader and you can immediately jump into the test.