But that's the whole point of security -- you're protecting precisely against the disguised malware, not the well-behaved software.
To say that this isn't necessary because there exist browsers that are well-behaved misses the point of security entirely.
And remember that iOS was built with a new model of security in mind from the start. They don't want their security guarantees becoming undone because suddenly third-party browsers can start installing things on the home screen that look like familiar apps and inherit all sorts of permissions.