That set is from 2005, not 2003. The engines are the same as the ones in the new catalog, as far as the bodies. The equipment inside is all different. The 2005 engines have AC Pullmor motors, TMCC and RailSounds. The engines in the new catalog have a different system, with DC can motors, LionChief Plus2 command system, and cruise contol, among other things.
The Williams Golden Memories F-3s are 13" long, the same as Lionel traditional. Williams' old F units were a different mold, a bit odd looking; they may be 12" long, I don't know, I'm not sure what you've got. Regardless, in answer to your question, the engines in the set shown in the new catalog will be the same size as the ones in the 2005 Super Chief set.