If we're looking for someone just slightly culturally off kilter from their potential empire, might I suggest that given the lack of a unified Germany that a candidate need only not come from either Austria or Prussia and that a Napoleon figure could originate in any of the other German states with Bavaria, Saxony, Hanover are all good candidates for origins. Otherwise the Germanish lands of The Dutch, or as mentioned Denmark and Bohemia are all good locations for origin in my mind.
One thing to consider, assumably without Napoleon the HRE is not formally disbanded, Is this a potential vehicle for ambitions or is it so Habsburg wrapped up and unsalvageable that a new German Empire essentially replaces it?