I'm on the last few (Exodus is hard!) so I think I've finished with the Bosche "side plot." I only have a few suspicions, and am interested in the ideas of others, and if there is an accepted explanation within the Freespace community.
If Bosche is "allowed" to escape by GTVA Command, then they must know at least something about his goals. According to his monologue (#4) it is in an attempt to form an alliance with the Shivans. We know from Mission 32 ("Return From Babel") that the meeting between the NTF and the Shivans resulted in carnage inside the Iceni - presumably leaving hundreds, if not thousands of NTF personnel and an unknown number of Shivans slain. Only a few NTF survivors escape on the rescue transport, and it is presumable that the number of humans who were taken aboard the ST Azrael was relatively small - just Bosche and his leading generals and staff. We never resolve what happens to Bosche or the Azrael, as the transport is not recovered in Mission 33 ("Straight, No Chaser").
Further damning evidence takes place in the failure of the Colossus to crush the Iceni as it escaped in Mission 25 ("Endgame"). The Colossus' beam weapons failed due to "sabotage" by rebel sabotuers. They must have been skilled in avoiding detection - even though there are 30,000 crew on board, how hard is it to secure what should be one of the top priority systems on the ship? Unless they were under deep cover for a long time, I find it difficult to imagine the NTF infiltrating GTVA forces while they are losing the war. Most of the NTF personnel are defectors from GTVA forces, not vice versa...
Also interesting is the rescue of Lt. Commander Snipes (Mission 35, "As Lightning Fall"). We do not know what information Snipes has, he is deep within Shivan territory. Apparently he was onboard the Grall (a prison transport, perhaps?) and docked to the Iceni during Mission 25 ("Endgame") as it evaded the Colossus at the jump node into the nebula. GTVA Command and GTVI were willing to put you and two wings of fighters, including four advanced Enyries into a risky combat operation with a projected low probability of success. And Snipes won't spill the beans on what he has in his head. Perhaps more about Bosche?
As to Command letting Bosche escape at Deneb, it isn't so straight-forward, and I could see a botched job of insertion due to scrambling warships to repel the return of the Shivans. It is fishy, and fairly unlikely that you could have stopped the Iceni in a Myrmidon with just Rockeyes and Tempests. Maybe you would have been joined by capital ships who were "reprioritzed" and sent to Gamma Draconis...
