The crash on header comments issue is now resolved.[1] Regarding the removal of entire sections not being a cosmetic change, have a look at the comments on the original task[2] where this was introduced and if you still think that it should not be part of CC toolkit, please consider leaving a comment there, reopening the the task, or creating a new one. I guess we could also make it an opt-in/opt-out option via user-config.py.
[1]: https://gerrit.wikimedia.org/r/c/pywikibot/core/+/453302 [2]: https://phabricator.wikimedia.org/T140570