> Even if the cocoa fruit sugars are more expensive in the markets of Switzerland than other sugars, the cheapest source of sugar at the cocoa plantation itself is still going to be the "leftover"/"waste" fruit.
Not necessarily. Chocolate abhors moisture, so sugars derived from the fruit and pulp will need to be extensively dehydrated. Over some range of energy and capital costs versus refined sugar cost, it may still be more expensive to have "whole fruit" processing on-site than to import refined sugar for processing.
> If the recipe these Swiss scientists have come up with is good enough, producers could start to build "whole chocolate" directly near the plantations and better compete in that market directly rather than in the cocoa bean "ingredient" market.
Is the expense of sugar really what makes the rest of the production chain (roasting, grinding, and final processing) infeasible on-site?
> And/or such a process might open up a much larger market for shipping the whole fruit, not just the beans, and moving the expensive labor parts closer to the industrial hubs.
If you're contemplating shipping the whole fruit without processing, I think this would still be infeasible. The fruit is wet, which would vastly increase the shipping cost per kilogram of final chocolate. Shipping the raw fruit might also require a cold chain, depending on how likely it is to ferment or spoil en-route.
You can analogize this to bulk shipments of sugar, where as I understand it early-stage milling is done near the sugar cane/beet plantations to remove most of the moisture. The raw cane sugar is largely dry, and it can be cost-effectively transported to sugar refineries for further processing.