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

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