A "bootloader" is essentially a software implementaion of a programmer and to put a bootloader on any chip you would need an external programmer. The Arduino environment will also support uploading applications directly through external programmers (Duemillanove and other Arduino specific boards included). So once you have an external programmer (needed for the bootloader upload) you don't really need the bootloader anymore to program your sketches.
The Arduino core and contributed libraries are specific to a few AVR chips (AtMega series) so you should expect to have to port/rewrite the Arduino sources to match your AVR of choice. Some ports exists, but it is my impression that most (if not all) fall into the "development in progress .." category.
I would argue that once you reach the level of competence required to develop for other AVR's including porting code and working with external programmers you're likely to be better off with alternative environments.