Huh. Well there you go. I wonder if that changed recently or something.
In any case, selling exploration data isn't the sole way to get repped up with a faction, you can use any means to become allied, and I didn't go to a controlled station to get that particular permit. That's just not a requirement. I know for certain that Brotherhood of Terra Mater didn't own a station when I ground reputation with them to get the permit.
You are quite correct that you don't need a permit faction in control of a system or station to earn a permit. However, missions is by far the slowest way to earn a permit, yet it's nearly the only way left to you when they don't own a permit.
Bountyhunting, mining, and trade are all far faster then missions. If you already have enough exploration data, then this is an instant way of getting a permit. But you need the permit faction to own the station or outpost for all of these methods.
Actually, the fastest (non exploration data) way of all to become allied with a faction is to cash in combat bonds during a war or civil war. This doesn't need the faction in control of a station at all. You just need the faction to be in a war.
