The explanation for Mega Man's Crouching Moron, Hidden Badass behavior came about after some fans pointed out an earlier strip that indirectly/inadvertently gave an explanation. Dave Anez liked it and made it canon.
Bob's scarf being burned and tattered due to his suit being a scorched Proto Man costume was a minor detail that fans made up. Anez thought it was clever and included it.
As anyone who's read at least a year into the comic can tell, Anez's original plan for the comic was to turn it into a hand-drawn superhero/sitcom hybrid revolving around the titular characters. A brief summary of how it would've turned out is extensively shown at the end of the seventh year.
During the earlier arcs, David Anez toyed with the idea that Mega Man actually wasObfuscating Stupidity the whole time. As in "I was always smarter than I seemed. I just wanted to screw with my enemies." However, David eventually decided that this idea would severely hurt the main source of comedy (Seeing Mega Man act like an idiot when you know he's not just isn't as funny) and made him a genuine idiot who would only act smart when in fighting mode.