It seems that when you save the global (organization level) YAML config, all the comments are removed from the file.
That stripping action is irresponsible as it can remove essential information that the author of the change may have added to the entry, like reasons behind settings different options to these values.
My removing the comments you are causing conflicts between people enabling and disabling features of codecov without any knowledge of what is the correct one, when it happend or who changed it.