one line of supposition is that FAA wants a new application every time spacex swaps an engine. This would be problematic with superheavy + starship having dozens of engines. SpaceX wants to just do an application per flight and swap whatever hardware they need as needed. the other common line of supposition is that FAA is concerned with exclusion zones and physical security (keeping people out of the exclusion zones). either way apparently SN8 was the ship/flight that violated and triggered the FAA wrath. SN9 is just sitting around because of what already happened.