I can confirm this error. Tested with your repo and unfortunately with mine.
In my repo, the problem occurs after this commit, when a subdirectory of the en and the fr directories in content have exactly the same name.
After changing the name in one of the language directories, the error doesn’t occur.
Should I open a bug?
EDIT: after reading above mentionned post, I had the idea to create empty directories with same names in the third language dir de, and to my big surprise, the error doesn’t occur anymore.