Honestly Fermenter you would have to get a developer to respond to most of those questions, or search the forum for the discussion around the original decision. I wasn't part of that. But the decision was made to do it the way it has been done, so that is the information I shared.
Does MC have a key for every item? I'm not sure. TV Channels have a Key. TV Recording Rules have a Key. I'm not sure all records have a key, as they are not visible to a user, but I would also guess that they do. There was a little discussion on that at one time, but I can't find it quickly. In fact, if I connect to my MC Server using a Client, and then select a video file, right-click and select "On Disk (external)", the location can't be opened and the URL shows the file does indeed have a Key. See attached image. But I think that Key is just used for media file location, and not Cover Art association.
Have a look in the Cover Art sub-directory. All Cover Art files are named to match the media file name. Some are structured, some are not. For example, a TV show Season will have a Cover Art file named something like "{TV Show Name} - Season {Season number}", or more specifically in MC terms, "[Name] - Season [Season].ext". So the association is created using the media file name, without the path, and in some cases additional tag values. It is named programmatically, and MC does not use database keys for an association. Cover Art is separated into different directories for [Series], [Season], etc., in part for informational purposes I'm sure, but also so that no duplicates are created.
Yes, there is an "Art Address" for every video file. It is stored in the [Image File] tag. If you really wanted to put all Cover Art under the Cover Art sub-directory, you could move the image files and edit the tag to point to the new location. But you would have to do that after using the "Get Movie & TV Info" function, and any other Cover Art functions, because MC will put any found Cover Art next to the video file and overwrite the tag with the new location.
I've never imported an optical Disc into MC, let alone tried to add Cover Art to it, so while the Wiki says it will be placed in the Cover Art folder, I have no idea how it gets structured or referenced. But the [Image File] tag would tell MC where to find it.
The MC database is not a Relational Database. It does allow fields to be marked as relational to a few select fields, such as [Series]. That is done programmatically, not in the database.
But if you solved the Cover Art file problem that you have, so that the files didn't clutter up the directories that the videos are in, what would you do about the Sidecar files? You don't have any option to move them to another location, and their creation, editing, and management is all handled programmatically. I guess the other devices you are using don't display XML files, so they are not a problem? Could you get those devices to also not display images in the view you are using?
Anyway, I wasn't privy to the reason behind the way video Cover Art is done that way. I just read that there were problems with the incorrect Cover Art being displayed, because of file naming, which is used as the key to find Cover Art.