So there are as you have identified a number of ways to go about it, but if you look at the upgrade section of the documentation, there should be an indication of the files that have been changed/added/deleted based on the version from which have upgraded. Effectively, if the new files overwrite the old files, then only need to delete the "extraneous" files and verify that overridden files are/have been upgraded as well.
I have to say, I was obviously in the weeds of things when I wrote last... Categories... Sheesh, too much into writing some new code and thinking abstractly rather than specifically. :)
But as for some form of "autoinstaller" or autoupgrader, there are too many potential differences to effectively develop something like that at this time. Maybe if the core code becomes uneditable or fully overridden through the use of notifiers and observers, but until then it is my opinion that there are just too many possible differences that could exist in a file or set of files. There is the database upgrade that is performed through zc_install, but not an equivalent file editor.



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