For the badges, I always thought of it as your Pokemon respecting you more for having them. A high level Pokemon wouldn't listen to a trainer with little to no badges because your badges are a measure of your skill as a trainer. Then again, do Pokemon even understand the Pokemon League? Who knows. I agree, it's a little stupid.
As for this;
Well you never went back and closed up the way to get to her did you? You certainly can't reseal the walls you broke to get there. So, the same way that loser with the shitty hair got to Luna.