This seems to be more of "don't paste garbage into a terminal, especially as root." With a sidenote that it might be safer if your custom application command interpreter didn't use > as the prompt character. I note that Bourne shell defaults to the safer % and # characters for the prompt. The # character for root is especially safe.
Yeah. About the only relevant bit is that root prompts tend to use # as part of their prompt precisely to inject a comment character in case of mis-quotes/pastes.
Wow I never heard that! I always thought it was just some arbitrary convention I guess.
I _think_ it started becoming commonplace around the early days of X11, although to be fair # and $ are neighbors on pretty much any keyboard layout.