How to upgrade SQL Server 2008 R2 RTM to SQL Server 2012 SP3 on the same server?
Unless you have user-created objects in the system databases, I would not try to restore them.

In fact, if you do have user-created objects, I'd script those out and add them into the new system databases as part of the restore process.

Some of the views, functions, procedures, etc. in the system databases may have version-specific code in them, so it's safest to just use the ones from the new version you're installing.