1. Being a Heroic Spirit, let alone being able to use a Noble Phantasm, does not mean a Heroic Spirit has the ability to function as a magus. See Kojiro as a good example.
2. And?
3. And?
4. The events of Fate/Extra and Fate/Extra CCC do not occur in the same, um, dimension as Fate/Stay Night. Timelines diverged after the 3rd Holy Grail War, correct?