They can't come from the City Line because it'd be at the wrong level. The City Line feeds into the present Cardiff Central station, which is of course elevated and passes over the Callaghan Square on a bridge. The shuttle to the bay will run on street level from Callaghan Square, on new platforms that would effectively be the "low level." Trains coming from the City Line and into the main station would have no way of getting to road level to join the tram tracks to the bay.
So it'd be a bit like trying to turn Snow Hill lines services from Birmingham Moor Street onto the line to Wolverhampton or New Street at Smethwick Galton Bridge, if you're familiar with that area.