I'm trying to think of regions where water-based high elevation gain might be at least within contemplation.
If canal technology had improved at the same rate and we had a magical economic way of building canals over huge mountains, like the one described in the article, of course we'd contemplate building more of them. Connect Denver to San Francisco, connect the Amazon to the Pacific via La Paz, connect Buenos Aires to Santiago, connect the Brahmaputra to the Pearl River over the Himalayas, connect Nagoya to the Sea of Japan via Kyoto.
New Orleans connects directly to Minneapolis, Chicago, much of the Ohio River Valley, I think to or near Omaha, up the Red River along the Texas-Oklahoma state line, and via the St. Lawrence Seaway to Toronto, Montreal, and ultimately the North Atlantic.
Central Europe has river transit from the North Sea (Hamburg, Amsterdam) to the Black and Baltic. Russia similarly has water routes from the Baltic to the Black Sea.
Much of the problem with routes such as SF <-> Denver is lack of water. The Great Basin is dry. The watershed for Los Angeles extends east 1,500 miles, to Denver, via the Colorado River, which is bled dry before it reaches the sea.
Further north, the Columbia-Missouri rivers nearly meet, and the dream of Louis & Clark could possibly come to be. Rail just happens to be far more practical.
Where?
It's definitely not out of favour here. We are a water nation, but inland shipping for cross-border transport is at the same level as road transport, and an order of magnitude more than rail transport. https://opendata.cbs.nl/#/CBS/en/dataset/83101ENG/table
We've got the Rhine, but that's hardly the only navigable big river in the world. One of those has much more carrying capacity than a railway and a lower cost.
Dealing with BNSF and Union Pacific Railways is much more costly and complicated for your freight than getting a barge to transport it out to the Pacific Ocean.
This is also why the farmers here are so opposed to dam removal. There are lots of small silted up hydroelectric dams that serve no other purpose today besides making the upstream waterway navigable by boat, which you need if your trying to dodge the high price of trucking or train transport of your crop.
> Up to 240 million tonnes of bulk goods are transported per year via the German Federal waterways, which amounts to around 65 billion tonne-kilometres. This equals almost 75 per cent of the goods transport by railway in this country or about 14 million lorry journeys.
Says over a quarter of freight goes by boot. Not surprising, seeing as how many small inland ports there are.