> It seems to me that it makes sense to upgrade such packages.
> The upgraded package can be installed in the user's directory.

They won't be automatically marked for upgrade when typing U, but they can
still be upgraded.
If the user marks a newer version for installation from one of the Elpas
it'll install just fine, and from that point on it will be marked for
upgrades like any other package.

> This scenario was always a goal of package.el -- to let some packages
> ship with Emacs or in the distro, and then to let users install new
> versions themselves by when convenient.
>
> It wasn't clear to me from the commit if this ability still exists.

Yes, the message should be more clear. These external packages are being
treated the same way as built-in packages have always been treated. This
means that (1) the user can indeed install a newer version if desired, and
(2) as long as they don't install a newer version it won't be automatically
upgraded.

Do you think these external packages should instead be automatically marked
for upgrade?
I think it makes sense for them to be treated the same as built-in packages.