You can enter a docked ship regardless of permissions that are set on the main ship that ship is docked to.
The end result is that you are able to enter parts of a ship regardless of its permissions required inside the faction.
So stuff like generators turrets and docked drones can be griefed by rank 4 players. (the lowest rank)
To reproduce:
1. Make a ship and put a faction module on it
2. Get another player to join your faction
3. Set that ship you made to founder required permissions
4. Dock a ship to the main ship
5. Have that low rank member enter the dock ship