On Melbourne's rail network, not many stations are located directly above a road (eg Richmond) and not many stations are completely cut and cover (eg Box hill).
Hmm I wonder why?
More difficult job to do -> takes longer to construct -> more disruptive -> costs more
Now in the case for the elevated stations along the Dandenong line, realigning the stations to go over the roads would of been the "perfect scenario", but not the most practical cost effective solution, since the slight benefit to have connection of both sides of the roads, would not worth the extra expense of the extra disruption, a more complex design and making it take longer to construct.
It's like the Buckley Street debacle, it's road under cause they take the most cost effective solution, not the "perfect scenario". It would be nice if they re-graded the rail bridge above, and put in a full blown trench. But is it the most practical? Nope.
As it is the Dandenong level crossing removal are actually a more "perfect scenario" already.
1) All 5 stations are now premium (escalators, toilets, staff and everything) and have huge structural piece for shelter.
2) The elevated structure doesn't dip and rise, it has long stretches of elevated rail. Yes it's possible it could have been just a 9 seperate rail bridges. How? Well if you look at the 3 Bentleigh crossings where it dip and climbs, the roads are at least the same distance apart as the ones along the Dandenong line.
3) They are the most expensive ones out of the other grade seperations (with exception to Main Road St Albans (200 million?)). Roughly 178 million each crossing. This is because they expanded the scope, to completely build open spaces, whole bike path, and build really fancy stations.