i know this thread is quite old but i found it through google and it may help others who are still looking for the same thing.
over the last few months i wrote a program that automatically turns epub manga and comics into cbz files, including correct reading order and direction, page alignment, metadata like chapters and more.
it started out as a python program, then a c# console program and is now a c# gui program. so if anyone is still interested in a niche use case like this, please try it out.
https://github.com/bust4cap/epub2cbz-gui