@amz - you are correct in your impression. Though I would suggest one of the reasons that Calibre does not update metadata within the book files in its library is that it doesn't matter what it is like in there for most users. You are a Kindle owner I see with mobi formats - when you send the book to your Kindle the metadata will get updated at that point. So it should not matter whether you try to update the book metadata before then?
If you are happy with what you are doing then carry on, don't mind me. If you have an awful lot of books you might want to trim out some of the steps that aren't strictly necessary