How does time "add up" for observers outside of and travelers inside of a Krasnikov tube? A ship travels 99% of c from Earth (leaving at Time A, say 2016) to Destination Star (arriving at Time B, say 2020, accounting for relativistic effects) to stretch the tube, leaves a buoy at Destination Star, then uses the tube's topology to return to Earth, effectively faster-than-light, moments after it left, according to how the Krasnikov tube is supposed to work (Time A plus a few minutes). Can the ship now return to Time B (2020) from "Time A (2016) plus a few minutes" using the tube just as quickly? If so, would its return to Time B mean "Destination Star in the ship's year 2020, the moment when it arrived / first stretched the tube to this destination?" And if so, would it mean returning to the system "before" the ship dropped the buoy?
My understanding of a Krasnikov tube is that it's a theoretical means for FTL travel that doesn't violate causality, because a ship traveling along the return path of a tube "rolls back" time to just moments before the ship originally left.

Now, I understand that there is a way to construct a return tube that would violate causality (http://arxiv.org/pdf/gr-qc/9702049.pdf), but let's assume for a moment there's some "chronology protection" in place that doesn't allow that to happen (the tube implodes when you try to do that), and that the question of the exotic matter needed to create such a tube isn't an issue for the ship's makers.
The questions I have then are:

A) Am I even thinking about this correctly? Where have I messed up?

B) I don't understand how a system of Krasnikov tubes, as some sources suggest, could be used to create an interstellar network for FTL travel. It seems to me that the traveler in the ship can never actually have an impact on his exit or return points, since he will always be returning to Time A (2016) moments after he left, or Time B (2020), the moment he arrives?
I think one of the most important things you missed in this article is the bit where they say the energy requirements are &quot;unphysical&quot;.  This is no different from saying it's impossible from our point of view.
A couple of quotes from the article :

Here as well, it was found that the wall of the “warp bubble” surrounding a spaceship must be unphysically thin compared to the bubble radius
Estimates of the total negative energy required to construct Krasnikov tubes of even modest dimensions were shown to be unphysically large.  Similar difficulties have been recently shown to plague warp bubbles and wormholes.  The Krasnikov tube suffers from some of the same drawbacks as these other pro
posed methods of faster-than-light travel, and is hence also a very unlikely
possibility.

The model you're discussing is really best thought of as a mathematical exploration, rather than a practical proposal of any kind.  I would suggest the authors are disproving the viability of Krasnikov tubes rather than anything else.  What was done was to try and fix problems with the previous model, but in doing so the authors ( to their credit ) show that they cannot bypass the fundamental problems making such a system unrealisable in practice.