According to the FAQ (downloaded while the link still worked
)
http://forums.subterfuge-game.com/viewtopic.php?f=10&t=1973If I try to target a sub which is going from Outpost A to outpost B, but there is another sub behind the main targeted sub, will the Pirate intercept with that sub first or will it bypass the others to reach the main sub?
He will bypass all but the targeted sub. In this perspective, Pirate’s sub does not count as between outpost A to B in this scenario, even though the route is exactly the same.
I believe I'm quoting Niverio here.
The Pirate is smart and navigates expertly around straight-line subs
[Edit]
A fellow L2 member confirmed in a recent game that the first sub gets bypassed on both legs of the trip