pert:
The short answer is that if you're running the same commands from the command line there is no difference. You can see the commands the Arduino IDE runs by turning on File > Preferences > Show verbose output during: > upload.Actually there is a small difference in that the Arduino IDE runs the second of the two Burn Bootloader commands immediately after the first, whereas if you're running the commands manually there will naturally be a delay between the two. This has caused problems for users of the AVRISP mkII and Atmel Dragon programmers in the past because those programmers take a long time to reset between commands and so the Arduino IDE may run the second command before that finishes. That problem no longer occurs for me with my AVRISP mkII using the latest AVRDUDE versions supplied by Arduino and I haven't heard reports of anyone else having the problem with that programmer recently. The problem is reported to still occur with the Atmel Dragon.
Ahhh, so technically I can do one or the other?