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Without iBooks for macOS, I don't think it's going to be possible to do updates. iBooks uses a separate App Store login. You may be able to use a mac at a store or borrow one from a library when needed since I think it doesn't rely on user admin priviledges, which would be required to add/change an iCloud login for a macOS user.
I do not know what happens when you update a book that does not have an added iTunesMetadata.plist. As mentioned, before iBooks always added that file but now it seems only after metadata changes are done within iBooks for macOS. I usually edit the keywords (subject tags) and that file appears. Afterwards, any change works fine while keeping highlights such as to HTML or CSS. All other edits such as to the NCX, OPF, or NAV also work, even renaming or adding files, as long as the file order and number of files in the beginning remain the name (if you're concerned about highlights) but don't appear until the iOS iBooks cache is reset.
If you want to try it, the folder on macOS is ~/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents/. Use terminal and unzip over the files.
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