If you manage the port, you can define which ships can communicate with it and prioritize dealing with one over the other. Imagine the queue of ships after the siege of Suez: if you own the ports that they visit, and some of them have strategically relevant cargo, you can determine the order to handle them.
Additionally, if you own the outlet, you can define when and how capacity expansions take place, so that it matches your strategy. For example, you can upgrade all of the niches you own along the way to a similar degree. If it only expands one outlet, the remainder of the line will be a bottleneck.
Although there are limits to this, as you’ll want to manage the relationship with shipping companies, it provides a strategic advantage when circumstances require it.