I like the name Southern Cross.
IMO it's like saying Grand Central Station in New York, or Central station in Sydney should be named after the street the main exits/entrance to these stations should be named after...clearly they are not.
Yes, but the differences are that the 2 stations you have named have been known by that name for a very long time, and as a consequence, most people know the names, even if they don't use the stations.
Also, the names have some logical reference to the stations importance, and general geography to the cities that they are in.
Southern Cross has no link to the area (Melbourne CBD), or indeed Melbourne in general.
The only links the name Southern Cross has, are to a historical event in Ballarat, stars on a flag, and a pattern of stars in the sky.