While there really isn't *usually* a good reason to update it manually, that doesn't mean you never open the app. If you accidentally block something, you can open it, and see what you've allowed and/or denied. Also, if you try installing an app from the market that already exists in /system/app, it won't install (unless you're updating it by putting a newer copy in /data/app, but that will only work if it's been signed by the same person; the same goes for replacing apps in /system/app without deleting them first).