I haven't combined those two expansions myself, but you are exactly correct -- the person who scores gets to choose which counting follower to move, so what you describe is exactly what I would do. Of course, if I scored a number of points that would put me on a dark space I'd have to choose if I wanted to move my victim meeple now to draw a Message or if I would rather wait to score a smaller feature before giving the Robber his points.
I think combining the sets would be a recipe for a stagnant game if there weren't many players. More players might be a little better, because with more players you might have a Robber following both of your counting followers, so then you could choose who to give the Robber points to. On the other hand, if you have a lot of players, the scoreboard would be meeple madness.