The NEL was the worst possible option. The amount of traffic it would dump onto the Eastern Freeway is obvious by the fact that the plans call for the freeway to be 12 lanes. Had it run from Eastlink before the tunnels to the current Ring Road terminus it would not require any work on the Eastern and it would leave the centre median available for a heavy rail solution.
As for your semis trundling down suburban roads, had rail remained the carrier of choice for all long haul freight (with trucks only for the last mile), there would have been no Francis Streets. But that's a failure for another discussion.
It's a myth that rail ever was or could be the "carrier of choice" for the low volumes and short distances of freight available in Victoria. For the first part of the railways' existence in this state they were valuable to the freight task simply because there was no other method of reliable overland transport. By the 1940s (probably even earlier) it was clear that road transport was at least as reliable as rail, if not more so, with the advent of better road construction and more powerful trucks. Moreover, it can be seen from VR Annual Reports of this era that the Commissioners were well aware that road transport was economically competitive as well. The only reason rail remained well-used for small volume freight over the next 30 or so years was a combination of direct regulation and rail subsidy.
At several points through the 70s and 80s, ideological decisions were taken to remove these incentives to use rail. You can argue black and blue about whether this was a sensible idea, but it had very much the desired effect of killing off unprofitable (in the traditional sense) freight rail, to the point where Freight Australia turned a profit shortly after taking over V/Line Freight.
The only way rail will again be used in any large-scale manner for the kind of small-volume freight that is the major contributor to "trucks on suburban streets" is by reintroducing subsidies and direct regulation. Again, this would be an ideological decision prioritising social and environmental benefits, but it would also have to be economically justifiable by reducing congestion. Certainly there is no real appetite for this kind of thing at the moment from either side of politics.
Returning closer to the scope of this discussion, the NEL business case assessed freight rail investment as an alternative. The specific projects envisaged were additional freight capacity through Craigieburn and intermodal freight terminals, and a spur line from the Hurstbridge line to LaTrobe NEIC. It is profoundly obvious that this option was not meant to succeed, given it was costed at $60-$75 BILLION (yes, really) with operational costs of $2 billion p/a. Yes, really. V/Line currently maintains 3200km of track and runs passenger services on a $600m budget, and the road lobby would have you believe running a couple of intermodals would cost three times that.
What's quite amusing is that despite this absurdity the rail investment was comfortably the second-best outcome of the options presented, and, given that the business case was never intended to make a finding against the NEL, we can assume a sensible freight rail investment would probably have obviated the need for the project altogether.
And the take-home lesson? They didn't even consider Doncaster rail, probably because it's a boondoggle.