Yes, when using SCCM (or other third party tool) to deploy an agent upgrade, there is not normally any need to have a different process for doing a clean install vs doing an upgrade. (This generalization may not hold if you have some complex configuration or operational needs, but such situations would be unusual.)
As @BradAkers has noted, sometimes Windows Installer determines that it thinks a reboot may be appropriate after upgrading the agent. To avoid an unwanted reboot being triggered automatically, include REBOOT=ReallySuppress on the msiexec command line you use for installing or upgrading the agent.
Yes, the agent packages you download from FNMS includes the upgrade package as well.
I'm seeing a lot of requests like this recently coming through support on how to manage agent installations / upgrades through SCCM so I'm going to create a forum post that will include some information that we have already from official sources and will then open it up for others to reply on with their experiences.
I've started a new thread on just this topic -
This is a very common request and there isn't much currently available but I've collated what I can find and put in that post and would like others to add to it so that we can help anyone with the same request.