Hi,
update-plan only changes the templates in the swift but it also splits for user provided env and what templates provided. Your changes should be in user-files and user-environment. Also minor update does not apply any change in networking.
I really don't think the -e are not accounted to swift if are out of --templates, but if you say that minor updates is not doing any network changes that's ok.
I'm sorry for very late reply - no, there shouldn't be any update to docs, the files in swift are supposed to be hidden from the user. The extra environment the user is uploading - in this case network-environment - is placed into user-environment.yaml and user-files. I think we should just close this as not a bug.