First of all, this is an amazing tool! It broke my Sveltekit application due to some commands for the dev server being dependent on *.md files, but it did what it's supposed to (removed 100+ MB) and worked without any issues.
I generated a clean-modules-result.json and would probably start reporting issues to GitHub repos, but then had the idea that there must be some way to do this automatically. At least for findings with 100% certainty that they shouldn't be in node_modules e.g. coverage or test files.
Did you consider this yet?