The only way to do it really is to elevate the railway over the road.
Sticking the road under will affect too many side roads, especially the Nexans (Olex) cable factory and the bus bay at the station. Road-over is even worse.
Road-over-Rail is achievable but the level crossing is at the bottom of two hills as you drive along Maroondah Highway, requiring a long bridge to avoid too steep a 'dip' at each bridge ramp. Bus access would also be an issue, as Lad_Porter has mentioned.
It also does nothing for the rather low-clearance John St bridge, which would need replacing or augmentation when the line is fully duplicated.
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