Sure, it's probably 'more efficient' now to load/unload cargo than then with automation, standard containers etc but then again back then you could use cheap labor (I'd guess in that part of the world very cheap) and safety would be a minor consideration so I wonder how much the equivalent cost differential really is.
Also the enlargement if I recall correctly is basically the building of new locks, and improvements to largely pre-existing channels. While a major undertaking, in real terms it's probably not as big as the original construction. Plus I seem to recall many of the techniques/much of the equipment used to build the original canal was in its infancy or had to be developed specifically for the canal at the time. Now I believe all the required technology etc exists and is fairly mature, so I'd expect the risk is somewhat lower.
Plus I wonder what the cost of the improvements that would be needed to docks, transport routes, pipelines etc to allow transport by land would be. Would it be less than the planned improvements to the docks?
Ships are already queing at the canal so could we assume that if the infrastructure already existed to send the cargo by train etc that they'd already be doing it.
Moving cargo by ship is still one of the cheapest/most efficient ways per mile so that needs to be taken into account.
As I eluded to above if I recall correctly part of the reason for the canal was to allow major units of the US Navy to get from Atlantic to pacific quickly. This probably isn't a big consideration this time but you never know what's hidden in some legal document somewhere.