Are you saying that I can get an Atmega 1280 without the bootloader, and then burn one myself? Hmm, perhaps it's time I get a programmer then...
And once you get the programmer going ... there is no need for a bootloader. The bootloader is just an on-chip "programmer" that lowers the threshold towards getting started with development.
The bootloader may of course add value as a field upgradeable system, but you could also bring your programmer along for the upgrade. The programmer has its own USB interface, so you may even skip the USB/serial chip for custom designs when there is no need for USB connectivity for other purposes besides program upload.