You're missing nothing. Dockside direct ship-to-train would be used primarily for transport to "inland ports" like Chicago or Kansas City where the boxes would be transferred to trucks, not other trains. The boxes are still drayed (trucked) to off-port intermodal yards for the reason you note, or even just because the railroad doesn't have a significant presence on the docks at the moment. They also get trucked to warehouses and transload facilities within a few hundred miles, in places where the land and labor are cheaper than near the docks, where the international containers are unloaded and repacked into trucks and domestic containers for train or truck onward moves - the "Inland Empire" portion of the LA Metro area is a major destination for truck trips from the LA/LB ports for that purpose. Then, for practical purposes, it's often more time- and cost-efficient for containers to be trucked to the final destination if it's within 500 miles (sometimes even more) of the port; a substantial number of inbound containers in LA, for instance, are going to places in the "Basin" for actual use, not just transload.

Logistics is a pain. I've worked with people who plan it and deal with the various carriers; they get paid a lot of money for their expertise, and they earn it. For many people, logistics means dropping a package off or picking one up at a UPS or FedEx store; as with many things in life, it's more complicated than that.