I really liked the whole "smoke screen" tactic. I had heard about this before in WWII naval novels I've read, so I enjoyed actually recognizing the tactic when Chandler brought it up. Meanwhile, does the Nathan James not have a chief engineer anymore? We've seen none at all this season, and Commander Garnett, despite being the XO, and even referred as such in this episode is back in the engine room, even though as XO she should have been on the bridge, what with Chandler being in CIC and everyone else off the ship. I know, the XO from the other ship was likely covering on the bridge, but it still seems very strange there's no apparent chief engineer on the ship anymore.
There's no rule against Garnett doing both jobs.
The XO has a straightforward function: To back up the captain and keep order among the crew. That's not a job that requires her to be in a specific location. She can be XO anywhere, including the Engineering spaces, where her greater expertise can be put to good use. Anyway, it's not uncommon for an officer to wear more than one "hat" when part of a small crew.
Although, one major issue that now comes up is, who is going to take over as CNO or even running the military? Slattery's the next highest ranking Navy officer, I guess, and they can easily stick Captain Meylan in command of the Nathan James, but what about the rest of the military? The only officers left with any real rank from the other branches were the ones that were somehow involved with Allison's plan. And while some, like the general from last week renounced their involvement and switched back, I can't imagine President Oliver is going to place very much trust in them.
He doesn't have to. The choice isn't as hard as you think.
Chandler's official title was Chief of Naval Operations, but his status as head of the US Military was solely a matter of President Michener's wishes. Rank and seniority were secondary concerns. Oliver has the same option. He can pick anybody he likes (Slattery, Green, hell Tex if he were still alive and wanted the job) and declare them head of the US military by virtue of the fact that they act on behalf of the Commander-In-Chief, and nobody can complain about it until they reconstitute a Congress. In fact, not even Congress could complain if he just named the person National Security Advisor.