Sure, but it doesn't have to be how "git clean -d" works. In particular, "git clean -ffd" could be more forceful, or there could be another option or a third level of force beyond the current two levels.
It really comes back to this question: "How can I avoid the failure, given that I am running 'git clean' from a script and not interactively?" The only answer I could find that's not unreasonable is to parse the text output of 'git status -s' to find the untracked directories and then run 'chmod -R u+w' on each of those directories before running 'git clean -d'." I can do that, but I still think a "force" (or other) flag that really forces the cleanup would be preferable, especially given that this isn't a completely idiosyncratic scenario but one that will happen more and more as go modules are adopted (unless go is changed to stop putting them in read-only directories).