Ultimately private business would help with the costs of moving the line underground, and as part payment, receive access to the new development land made available.
The idea of cost vs. benefit has interested me for a while. At some point in time someone thinks of an idea that seems like a good idea, but it turns out to much too expensive. Eventually that idea will come back again when it turns out the benefits outweigh the costs.
For example, diging through old rubbish tips for antiques or even old toys and selling the results on eBay. Sounds like madness, but if you could get $10,000 for an old Transformer you might start digging.
The cost of land in the inner city is so much that spending billions on moving a train line stops seeming so crazy.
Removing level crossings at four middle-inner roads would be fantastic, as would, I expect, the reduction of rail noise to those poor poor inner suburb people who built their mansions so close to the trains. Their house prices should skyrocket, assuming the tunneling doesn't cause too much damage. Assuming that the space isn't filled with something worse.
Unfortunately, moving the line underground rules out any chance of extra lines to Glen Waverley. Something I'm sure will be needed soon. Of course we could always just rip down the new houses and businesses and build more trains on top. Ha.
I'd suggest building another couple of lines into the tunnel, and build them high enough to accept double decker trains while you're at it. Is it too expensive now?
Meanwhile...
One nice suggestion I heard recently involved pushing inner city residents onto trams (or bikes, or taxis) and shutting down inner city train stations, moving the focus of trains to large scale outer-burb people movers. I'm not sure what they meant by "inner".