The choice between the Construction Bay and the Greenhouse have drastically different chronicle sheet rewards. The Brakim Admittance boon is a top-tier reward, but Iztheptar Research is completely useless for anyone who has a permanent Personal Boon (such as an existing race boon). On top of that, the boon itself is kinda circumstantial. You get a bonus to Fortitude saves on a disease or hazard if you've already made a save against it? How often (outside akatas) do you actually roll twice against the same Fortitude hazard? How often do you know that such a hazard will exist while slotting your boons?
If there were some indication that the Construction Bay was the "correct" choice (i.e. it was more heavily defended, obviously a harder target), then I could understand. If VC Naiaj said that you better be ready for serious fighting if you go there, then okay. But she attributed equal interest in both targets, and the Greenhouse seemed like the curious "what's up with that, what do the Space Nazis want with a bunch of plants?" choice.
Of course, none of that would have been necessary if the reward for the Greenhouse was an Admittance Boon instead of a questionably useful Personal Boon. There are five other races in Escape From the Prison Moon that would be acceptable; Neskintis, with their bonus to Life Science and Survival, seem like the obvious choice for a greenhouse.
Moving on, the fight against the Azlanti captain is a bit anti-climactic as well. Placing a BBEG caster in a close-quarters fight is never going to end well for the enemy. That room barely has room for the PCs, much less a dynamic battle with spells going off.
The "loot hunt" at the end also needs a 4 player adjustment, because it's needlessly punishing against small groups, who may have only one person that can roll for the length of time available to loot the ship, or any of the individual checks. My group had three soldiers and a technomancer, so our skill options were somewhat limited.
Having each check take 10 minutes also feels needlessly game-y, since there are existing rules for how long most checks take (a Search check is 1 minute per 20' x 20' square, if I recall). Having each check be 10 minutes, when you have less than 10 minutes before the ship blows up (or whatever) just takes players out of the game and feel railroaded (my experience when players are "on the clock," as it were, is that they don't mess around with searching until they clear the hazard without being beat over the head with phony time limitations).