First , why have you linked the 4.2 guide and the 3.1-4.1 guide? The no vulnerable IOS guide doesn't require running apps from the HB. The instructions are to bannerbomb dop-mii.
Which is also what the user could do with any of the apps at any time when following the guide. Messies guide even has you load the apps from bootmii I believe.
I don't know the entire situation but this is what I do when they won't run from the HB or I can't access it. Load via BB Bootmii or Priiloader.