(I'm hoping Singer would have ditched the ridiculous, tentacled floating head of STAS).
The "Skull Ship" originated in the comics in 1983. They didn't actually use it in S:TAS. Brainiac's starship there was a giant wedge-shaped vessel. The only appearances of the Skull Ship in the DC Animated Universe were in the Static Shock
episode "A League of Their Own, Part II" and in the Justice League Unlimited
episode "Divided We Fall."