Running missions that the game offers you to do is not an exploit.
Deal with it.
It might not be an exploit, but it, like the other disasters before it (rares, Robigo, Sothis, Ceos, passenger missions), seems to point with FDev having difficulties balancing anything effectively, not thinking things through, and then leaving such legal loopholes in for far to long, to the detriment of the game.
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Land on a small pad? Small fee. Land on a large pad? Large fee.
You jest, but time-based berthing fees were in the previous two games. I see no reason why such fees (and things like local taxes on trading goods, that can be 'got round' through reputation and NPC interactions) aren't added to the game.