Updating apt get
However, there are occasional changes made in the Foundation's Raspbian image that require manual intervention, for example a newly introduced package.
It is available on the Debian website at will install upgrade files in place, even on a running system.
But why get the Software Center at all, if the goal is to install updates via the command line?
(None of the subsequent commands you recommend require the Software Center, nor do any of them use it or benefit from it if it's installed.) Note also that it seems unlikely this will keep the "packages can be updated" message from appearing.
In case there's some important note to add to the upgrade process, the packages will alert the user, and often provide a solution to a possible problem.
You should also read the Release Notes document that describes the details of specific upgrades. Or you can use the redirector service httpredir.which aims to solve the problem of choosing a Debian mirror.