Somewhere in the mid 8.6.x.x versions the upgrade scenario stopped working as it used to. I just tested in 8.7.0.0 and it's still an issue so I figured I would report it.
The way that I generally perform upgrades is to simply change the path that /admin is pointing to. So it could be from 8.6.1.14 to 8.7.0.0. The root of the site points to a custom Application folder, but the /admin folder points to a shared copy of the application downloaded from the developer portal.
On the first visit to sitename.com/admin after repointing the /admin folder you'll get a warning that the versions are different. In the past it would automatically copy the files from the /admin/../bin to the site's /bin folder. However, a few minor revisions ago that stopped working and it doesn't appear to work anymore.
Now I have to manually upgrade by copying the files myself. It's not that difficult but it was much more convenient previously when the upgrade was taken care of automatically.