I may be wrong on this, but I'm sure you'll find that the banners would only be Imperial or Ducal if they were in the service of Maximilian, or the Duke of Burgundy (Charles V as he would become. Maximilian was only Duke when Mary of Burgundy was alive and inherited nothing after her death).
I assume therefore that they would use the standard of their leader and/or the flag of who they were serving, in this case some variation of the English battle flag.
Likewise, the flags and banners of Low Country cities and areas, would only be borne by contingents raised from, or hired by, these respective communities and not merely borne by mercenaries raised in them, but serving someone else.