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.