Using the ATMega328, from an Arduino UNO in a Standalone configuration, and bootloader - I am really lost
So do I understand you correctly that you want to lift the ATmega328 IC from the Uno board and use it on a breadboard? That strikes me as an unnecessarily risky proposition just to save a dollar or two for a separate ATmega328p.

Second, you technically might not have to write a new boot loader to the chip, if you don’t intend to reprogram it while it’s on the breadboard, but you definitely need different fuse settings, and the two changes are closely related in the Arduino IDE.

Third, bootloaders on ATmega are incapable of modifying themselves, so if you want to write a new bootloader, you always need a programmer (which can e.g. be your Arduino UNO running the ArduinoISP sketch or ScratchMonkey); I don’t think your single-microcontroller idea would work.

For mass production, you’d just use a programmer. Bootloaders tend not to be used for this, which can lead to situations like this year’s mishap at SparkFun