The cliff gaps are filled with the doodads called "[...] cliff gap filler".
I don't get the second issue... the cliff type shouldn´t have any influence over the terrain height. If the ground is at the same cliff level and the ground height wasn´t altered, both sides should be leveled.
println already has made a couple of tutorials for his tool, and it's completely documented in github. He was offering to give further and personalized help for anyone interested.
Blaming him for not sharing even knowing that he has programmed, documented and maintained for free one of the most (if not the most) useful and complex modeling tools for sc2 during the last 3 years is unfortunate.