Samuel Lijin [off-list ref] writes:

After some more digging (and familiarizing myself with the
behind-the-scenes logic) the issue is that dir.c has this implicit
assumption that a directory which contains only untracked and ignored
files should itself be considered untracked. While that works fine for
use cases where we're asking if a directory should be added to the git
database, that decidedly does not make sense when we're asking if a
directory can be removed from the working tree.

Thanks for digging.

I'm not sure where to proceed from here. I see two ways forward: one,
builtin/clean.c can collect ignored files when it calls
dir.c:fill_directory(), and then clean -d can prune out directories
that contain ignored files; two, path_treatment can learn about
untracked directories which contain excluded (ignored) files.

My gut feeling is that the former approach would be of lesser
impact.  Directory A/ can be removed "clean" without "-x" when there
is nothing tracked in there in the index and there is no ignored
paths.  Having zero untracked files there or one or more untracked
file there do not matter---they are all subject to removal by
"clean".