Can somebody explain to me what are the benefits of Android System App over a \"normal\" app (besides that fact that a system app cannot be uninstalled)? Special permission
From your explanation I guess you mean the the pre-installed applications (like the Browser or the Messages app). You can take a look in these apps at https://android.googlesource.com. (search for platform/packages/apps/...).
You will find that these application are no difference to your own custom developed Apps, except you can't remove them. They cannot be removed as they provide the basic functionality to operate your phone / device. So, same security constraints apply there.