The Acrata was not the Thanatos, it was a much larger and more powerful ship, a flagship, many more soldiers and officers would be under its command. The navy had suffered a severe setback with casualties from the last battle, so much so that many of Eneas' former officers were assigned to take command of their own ships.
Of his old team, the sub-admiral was only able to keep Ajax, and Orpheus was lucky enough to reinstate Horus, even if it was temporarily for this mission. The real problem came to complete the double functions of all the command bridges, even assigning one bridge to Horus and another to Ajax, as they were leaders of mecha squadrons, he did not know who to trust among all the young people in front of them.