During their extended stay on Planet Omega, some of our heroes found an ancient cybertronian device that, when paired with the Omega Key, could scan and deconstruct objects to augment Salvation with new features and technologies. In addition, it seems the Omega Key took the liberty of making a few changes to the Fleetcarrier's design of its own accord.
The first of these changes is the complete redesign of Little Iacon- the main hangar has been rebuilt into a spherical chamber roughly five miles in diameter, holding the miniature city within it. Hovering in the middle of this chamber is a large hologram of the Allspark- Primus' life-force- with accompanying holo-screens reminding our heroes of the declining health of their dying god. Smaller Allspark holograms can be found all throughout Salvation, projected within glass orbs embedded in walls and consoles.
Hangars thirty-one and thirty-two have been replaced with a new room at the rear of Salvation, containing ancient cybertronian machinery designed to be used with the Omega Key. So far, it has been show to project a larger version of the map in the Key's datatracks, produce Blue Cybermatter, and possesses a console similar to the one in Planet Omega's spaceport- the one that allowed our heroes to scan objects to upgrade Salvation. This room likely has other functions beyond these, but they can't be accessed until more of the Omega Lock's pieces are recovered over the course of Salvation's voyage.
Salvation's maintenance tunnels now have a dedicated living space for the insecticon hive that took up residence within the Fleetcarrier at the start of her voyage. With Facelift's presence aboard the ship discovered by the captains, and after some negotiations with the mad doctor, the Butcher of Tetrahex now resides with the insecitcons, where they can keep their many, many eyes on him for the remainder of the voyage.
The Inquisitive Savant, the ancient cybertronian research and exploration vessel that our heroes found early on in their voyage, was sacrificed to improve Salvation's defenses, granting her regenerative hull plating and an energy shield that stretches over the entire ship. Unfortunately, the Savant's artificial intelligence was destroyed in the process, willingly sacrificing itself to make one final act in aid of our heroes and their mission.
Other augmentations include upgrades to Salvation's interior defenses, and improved engex distilleries for Antillian Sunrise and the Peace and Tyranny (not very useful in the grand scheme of things, maybe, but much of the crew certainly appreciates it all the same).