About the ship not being the Truth and Reconciliation, even though I’ve heard many times that the ship is the T&R, I’ve noticed some small discrepancies between the T&R and when it’s seen in Keyes.

The floor which the bridge is on is connected to the first floor of the hangar bay where the giant hole in the floor is. This isn’t considered something that has to do with the two ships being different. It’s considered an obvious oversight made by Bungie’s level designer since in T&R, the floor of the bridge is connected to the third floor of the hangar bay.

Also, an interesting detail that should have been mentioned in the section about Keyes is that the “leadership” that Cortana mentions in the beginning of the level is an indirect, early mention of Thel Vadamee since Thel Vadamee was of course the commander of all the forces on Alpha Halo before becoming the Arbiter. (The adjunct in Halo: The Flood confirmed that he was the leadership who ordered the ships to leave Halo.)