SpaceX is a commercial space company. Arguably, the first legitimate one (yes, Bezos and a few others have their companies, but none of those are fully functioning delivering satellites, payloads, and passengers into space).
Until very recently, ALL space launches and programs were handled by NASA and the government. ALL of these rules, procedures, and policies are in fact new. Many are legacy procedures from the hey day of the Apollo space program. For commercial space ventures to thrive there is going to need to be more fluidity of processes and procedures, regulations will need to be relaxed and made more reasonable. A simple change should not be reliant upon a 3 month period of time and to be told two days beforehand that they will not have time to address the matter. There should be a requirement that any change be logged to the flight plan. But it should not be dependent on a small government agency to micromanage every detail.
All these regulations and procedures are new for commercial space, and they need to adjust to the needs of a fledgling industry. (And filing a lawsuit is generally how you get change done in government + lobbying congress.)
If the FAA doesn't adjust, eventually what will happen is that SpaceX and the entire commercial space industry will move outside of the country. Either become entirely seaborn, or more likely pick a tiny island nation on the equator to build their spaceports. And they will just bypass the government entirely. This will eventually happen anyways.
One day, it will make more sense to simply mine an asteroid, 3D print parts, build spaceships in space, and have companies who are not bound by ANY nation. And don't get approval for deploying ships or satellites, only to land their ships.