The difference is that finals played at subiaco are there because either the eagles or dockers have earned the home ground advantage. So yes there is a disadvantage to you, that's the point.You can move some home games to the G if you want more games there, you can't really have any say in away games.
We only get to play Subi maybe once a year and yet have to front up for finals there at a huge disadvantage.
The Grand Final is a different kettle of fish as the Victorian side hasn't necessarily earned a home ground advantage.