Not from Geelong to Ballarat but from Sunshine west directly to Ballarat instead of taking the scenic route via Geelong. Sorry I didn't realise this was part of the murray basin standardisation.
That's the Ballarat RFR line you're referring to. It's got much worse grades and curves than the Geelong-Ballarat line, so it's not much good for freight despite the shorter distance to Melbourne. In the past (pre-RRL) it's had the odd BG grain train routed through it to get to the Port of Melbourne and before the Melbourne-Adelaide line was gauge-converted in 1995 it had Melbourne-Adelaide fast freights routed through it.
It's essentially a passenger-only line these days due to capacity constraints and its interface with the Metro network. Converting Ballarat-Geelong to SG will be the nail in the coffin for freight use of that line.
Bendigo Council have produced a freight plan; but any new development must include the ability to integrate LCL freight to provide a rail option. Using containers for everything you move is not cost efficient as the containers are expensive to rent and are not required or LCL which is a lot of freight.
That depends. Port-bound freight and vice-versa is going to come in a container no matter what. LCL replaces the cost of an 'oversized' container with the cost of a van wagon (which aren't as common as they used to be) and the costs of double-handling.
You may well be right that LCL freight is a lot of freight. You're wrong about it being rail-contestable though. Rail still works best for long(er) distance linehaul and export traffic, both of which end up having wagon- or container-load minimum sizes.
Marong makes no sense for a rail-focused intermodal. Access to the east coast ARTC network is too roundabout so it essentially rules out domestic LCL (or container) traffic. That leaves export traffic (containers) and possibly Adelaide/Perth traffic (too small to bother with in-and-of-themselves). It could be OK for receiving inbound grain wagons perhaps, but that's a pretty minor source of traffic and highly dependent on the type of businesses that reside at the Marong Business Park. It'll end up vomiting outbound traffic onto the Calder Hwy, not the railway line.
If you wanted to do a proper rail-focused intermodal development in Bendigo, put it on the Echuca line somewhere and campaign for a rail connection to the North-South ARTC corridor (either to the NE SG or Tocumwal line post-conversion). That would get you much better East Coast & Port of Melbourne access and as a bonus, good access to SSR's Bendigo North workshops (assuming they want/need SG access).