I'm just wondering if this group has heard of the infamous project proposal once known as 'Operation Double-Fault' - the plan to drop the Glen Waverly Line between Heyington - Glen Iris and then cover it with decks? If not, this article from 2007 might refresh memories http://www.theage.com.au/articles/2007/03/16/1173722750206.html. The proposed cost was $4 Billion for a total distance of about 4km's. Initially transport planners were sceptical, then they warmed to the idea, then the idea was dropped. This plan from S302 and his group sounds very similar and despite the best intentions of keeping services running while they construct the trench, even an extreme amateur like me can see this will be difficult, not to mention the 'choke point' single line service.
I think what this group fails to appreciate is that there is a huge cost in covering up railway lines, and in Melbourne it just isn't done because the economics don't stack up. Daniel Bowen has explained as much in this short blog post: http://www.danielbowen.com/2016/02/07/value-capture-over-rail-lines/. Not to mention the costs associated with extra safety systems that are needed with underground railways. I believe this group thinks that it's well-intentioned but much more research is needed. And then there is the Gas line that supplies 60% of Melbourne's gas. I don't know if this group has had a close look at the Ormond/McKinnon/Bentleigh project but even that is not going to be a full trench - the line will be close to ground level in between station due to old creeks/large drains.
Again, I understand this project brings concerns from some, but I think what they are proposing is very expensive and disruptive.