I'm using C:SV on my Fleet Armitage to attack multiple targets too, so dps figures in ISE shouldn't differ that much. But they do. My latest figures are 13k for Recluse (sci), 10k for Galor (eng), 8k for Fleet Armitage (tac), 7k for Temporal Destroyer (sci).
Also, I have been doing the same foundry mission on all my ships to farm ec and I am seeing a similar dps rate in terms of time needed to destroy a single Negh'Var. The Recluse and Galor are both than my Fleet Armitage with DHCs and Turrets.