simplesi:
So why not just upload your final sketches to the standalone (non-bootloaded chip) project when its working
(I'm sure that your method is good for some things but I'm wondering if people are spending time loading bootloaders when all they really need is to set the fuses to get their clock speeds right)
That's exactly what I do, see Prototyping small embedded projects with Arduino | David Crocker's Solutions blog. Having a bootloader installed on the final system increases startup time, and if you are using the internal clock then it probably won't work anyway because the baud rate will not be accurate enough. However, if your hardware need a serial port anyway, then you could argue that including the bootloader makes reprogramming it easier.