In theory, there shouldn't be much difference.
In reality, the "device programmer" needed to program a chip without a bootloader has historically been a major stumbling block standing in the way of users trying to use microcontrollers. Often proprietary and used with complex host-side software, often limited in their support of alternate operating systems, and often (significantly) more expensive than an Arduino itself. And subject to certain target-bricking errors (like setting the fuses wrong) that are not possible to make when using a bootloader.
The forums are full of people who have been unable to get device programming to work, even to the extent necessary to burn the bootloader into new AVR devices. Non-arduino forums have people complaining about having to switch firmware in their (official Atmel) programmers depending on the version of AVRStudio they're running, or if they're using linux instead of Windows. And complaints of sketchy but cheap programmers from eBay that may or may not work. And weird behavior when trying to program chips with large flash (mega2560.)
I mean... it's not THAT difficult to skip the bootloader and use an external programmer. But it's a lot harder than just using the bootloader.
(that said, the state of AVR programming using alternate tools is "pretty good." There are inexpensive programmers that are known to work well that are specifically aimed at the hobbyist community, and there is a lot of support.)