Ive done some more digging, it appears the journey planner on the above link isn't the best for giving out all options, and complicates the trip also.
Simply put Trains to Frankston leave Sourthern Cross Station every 15min the connecting bus 788 from Frankston to Portsea stops at Rosebud (suburb next to McCrae they might stop at McCrae if you ask nicely) leaves every 45min depending on which train you catch you could have a wait of 9, 24 or 39min for the bus which leaves from the Frankston Railway Station.
Train leaving Southern Cross to Frankston (Monday to Friday non public holiday)
10.31am arrives 11:36am next bus 12:00pm
10:46am arrives 11:51am next bus 12:00pm
11:01am arrives 12:06pm next bus 12:45pm
11:16am arrives 12:21pm next bus 12:45pm
11:31am arrives 12:36pm next bus 12:45pm
11:46am arrives 12:51pm next bus 1:30pm
12:01pm arrives 1:06pm next bus 1:30pm
12:16pm arrives 1:21pm next bus 1:30pm
12:13pm arrives 1:36pm next bus 2:15pm
12:46pm arrives 1:51pm next bus 2:15pm
These are not the only times the trains and buses run if you are travelling outside these time send me an e-mail and I will look up some relevant times for you.
I still think the limo option is the coolest, who dares to be the Limo travelling IC Rockstar