Not sure if I understand you correctly, but the height of the walls (minus house upper layer) is deliberately one 16 pixel tile high -- decided early on that'd be a part of this style and tried to stay consistent with that. I didn't understand you correctly, whoops! Not sure how I misinterpreted that.
I can understand how some people would prefer taller walls that overlap characters a bit, and that would actually be easier to draw as you don't have to break perspective/geometry to fit stuff in as much, but I'm sticking with how it is in this series.
I don't have plans for making adjustments at the moment. Sorry this part of the tileset bothers you!