However, do any of the changes involved in the 4.6.x upgrades involve changes in the db structure, or are all the changes in the code of the core drupal files?
There are some changes to the db, yes.
Because, if the db remains unchanged, and it is only the core files (ie, code) that has been changed, wouldn't it be possible to backup the settings.php file, unzip a fresh 4.6.3 release over the 4.6.0 release, restore the settings.php file, and be done with it?
So, I guess what I'm asking is: are there any db changes in the single upgrades from 4.6.0 to 4.6.1 to 4.6.2to 4.6.3?
Yes, there are changes and you need to run update 130 and 131 (as far as I know the 4.6.0 corresponds to update 129) to use the 4.6.3 without a problem.
What I wonder is why I cannot do this just by running them through the very last package.