I have a .cbz file with images in it that are organized into sub-directories within the archive. When I try to read them in YACReader, it will only show the images of the lexicographically last sub-directory. Is this the intended behavior? If so, what is the motivation behind it? If not, what is the intended behavior? Can this be fixed? Thank you...

The proper behaviour should be to get the full list of images ignoring folders, sorted them, and display them as pages.

My guess is that the files inside those folder have the same name, so the previous process overrides them....

If you want to first read folder1, then folder2, ...., folderN. Then I suggest to make a comic per folder, or put all the images in the same level and rename them to be in the right order.

cbr, cbz files should be simple, I don't like the idea of adding features based on the structure of the file.