When in the Software booth, you can buy Maps...it always deducts money, if you have that map already or not. I'm not sure about some parts of it, but you can even buy "all" maps when you already have all.
How about to start the count once you've actually bought the neat little thingy from the admiral?
Then the "knowing" player can fly around all he wants...and the story doesn't seem so "broken" apart...
-Fishion