As long as they stick to the same general engine, but with a Magic extension onto it, and just change the units, it shouldn't be too much to worry about. The time taken is probably more in the way of making assets than engines, but Total War already plays to a large part like Warhammer Fantasy Battles already.
CA do indeed stumble outside their comfort zone, but large-scale combat-strategy games are very much within it.
Games like Mark of Chaos were fun, but somewhat limited in scope, If Warhammer Total War lets you do the kind of battles that are impossible on other versions (usually because of Point limitations), maybe make it the story of Magnus forming the Empire, then it could certainly be a hit.
