You’re definitely right that a “good ending” where the players are able to recapture the Octopode and make it to Procyon B is not well supported in the text. The NDA arrangement is primarily meant to create some immediate friction with the Fox crew (and goofs), and hopefully lead to a more intricate and volatile situation when the raid starts.
As for the theme, we decided to interpret it a bit more loosely… we’ve got a seemingly tight knit crew, but with tension bubbling beneath the surface.
A note on the information ordering, when you open the cover to read the inner flap, the page headered Fox Uniform with the Vulpes diagram will be visible. Just a quirk of roll fold ->digital conversion. I have a version for screens that I'll put up after the jam period with a min. price