I've never seen this one unless you're doing a system restore, not a database restore. If you're rebuilding an instance, yeah, you'll need to restore system databases. If you're just restoring a database, restore the database. Don't mess with the system DBs at all.

As to replication and overwriting a database. Well, the easy part first, yes, I restore databases with overwrite all the time. That's not an issue, if you want to overwrite that database. As far as replication goes, this gets very tricky. If you're restoring a publisher and you're in transaction replication, you're going to have to rebuild the replication including a snapshot, etc., because you no longer have the two databases in proper syncronization. If you're in merge replication... you might be able to rely on the merge to fix up the databases after the restore (good luck). If you're in snapshot, nothing, another snapshot will be taken. But, all this needs to be tested & validated within your environment (although obviously not on the production systems).