The elevated walkway I added in order to placate the inevitability of a small but vocal opposition to the removal of the rail trail. It's very possible that they would raise a big stink about losing the trail, even if it's for re-activating the corridor for it's original purpose, without getting something in return. The corridor probably isn't wide enough to run 2 tracks and a pathway in parallel, so I figured elevating over the tracks was the next best option.
Overall, I don't think we've seen the potential impact of all of these rail to trail conversions yet. In the 90s and 2000s, a whole bunch of rail corridors were converted in this fashion, and there may come a time when they will need to be used again as rail corridors. However, I think significant battles will ensue over whether these corridors should be allowed to return to their original purpose.
On a larger scale though, I think this RER extension accomplishes a lot of valuable goals: It links downtown Hamilton to the Mountain (both existing and future development). It links the Mountain to the rest of the GTA via the RER line that would continue all the way to Oshawa. It turns the BLAST network from a long haul network into a feeder network, with every line connecting to the RER line at some point along it's route. It links to the airport, which would allow Hamiltonians, as well as people from Halton Region and even further east to use that airport as an alternative to Pearson, without having to drive there. It would also give the sprawl occurring on the Mountain some points around which to centre. Yes, you could say that this would accelerate the sprawl, but the reality is it's happening anyway. Might as well make it less dependent on long distance auto travel.
The corridor is already there, and by and large the grade separations, particularly along the escarpment, are already there. The most complicated part of the line would be the section from Mohawk Rd to Stone Church Rd, which would likely involve going under the Linc. Still, compared to an LRT or a subway, the cost per km of this line should be pretty reasonable.