That's the basic issue at the core of this discussion. Economies of scale will always win (in the absence of market-distorting regulations).
Personally, I think the CT "feel" works just fine in a TU with 100 kdt+ container ships. Just as in the real world you couldn't run a successful cargo business with an 80' tramp between Long Beach and Tolyo, you're not going to last long running a Far Trader between Mora and Vincennes. But conversely, just as in the real world you can run a successful tramp freighter business between backwater ports in the South Pacific, you can do so in Traveller between the backwater worlds of the Marches.