One of the main reasons for the flagship services leaving early is so that they don't get delayed by station-to-station trains that would otherwise get in the way. i.e. The Bendigo flagship leaves at 5:45am, and stop-all-stations trains follow at 6:15 and 6:30am. It wouldn't work the other way around.
One benefit is that if you want to then get to somewhere else in Melbourne before 9:00am, a 7:25am arrival at SCS helps! It's worked for me in the past. Perhaps they could consider two express services in the morning peak: The current one, and then another that gets to SCS at say 8:45am?
That makes sense, and I like that idea.
I do, however, see something like this done on the Traralgon line. There are four morning peak up services, all commuter; there are two morning up fast services, the 05:30 and and 06:39 ex-Traralgon services (arriving at Flinders St at 07:30 and 08:42 respectively); there are also two all-stops services, the 04:31 and 05:58 ex-Traralgon services (arriving at Flinders St at 06:47 and 08:25 respectively).
There are four evening peak down services, three commuter and one long-distance; there are three evening down all-stops services, the 16:10, 16:51 and 17:39 ex-Southern Cross services (arriving at Traralgon at 18:21, 18:59 and 20:26 respectively); there is then the only evening peak fast service, the evening down Bairnsdale (18:36 ex-Southern Cross, calling at Traralgon at 20:49).
I believe the Regional Rail Link will open up better pathing for regional commuter services, and hopefully we will see a double-flagship sandwiching on the Bendigo service. The problem with the 'flagship' model is that it can result in big gaps, such as the former gap of over 90 minutes before the Ballarat flagship had Ballan added; this can only be alleviated with frequency, but frequency limits how much we can skip-stop.