I dont know whether this is the real reason, but I have found the following syntactical use for nesting links in any diagram between (sort of) any element pair.
In some models it is clear what the intent of association links (and aggregation links) mean within the specific context of the diagram. For example, an association between two nodes in a deployment model adorned with the label <<TCP/IP>> fairly easily indicates a communication link. Now add another element - named "TCP/IP stack". I want to show that the stack is contained within one of the nodes. Using a nesting link clearly visually indicates to the viewer that I am talking about a different type of connection here.
Now, if we start to decompose the TCP/IP stack on the same diagram into a set of TCP and IP and linked list classes, the aggregation links convey a specific semantic relationship between elements that is again very different from the nesting link between the stack and the node.
IOW, I see the nesting link as a visual highlighter, yes representing "physical containment" but adding no other implied relationship.
By that I mean the following. Lets start with something pretty stupid, a class with an inner class that has no logical relationship to the containing class. Say class "fruit" with an inner class of "screwdriver". There is no logical association, or aggregation, between fruit and screwdriver. But there is a containment relationship, and one with no implied logical relationship.
Now we wouldn't build this class structure - well no sane coder would anyway - but if we stop the sillyness and talk about a more logical example. Consider class "tree" with an inner class of "fruit". Now there will be a logical relationship between the two - maybe even more than one - maybe even multiplicity is involved. These can be modelled using the appropriate association and aggregation links, each of which conveys that specific logical relationship. Now maybe the containment is unimportant from the POV of the model, and need not be included. Perhaps it is even implied somehow in the diagram. But if I want to explicitly talk about this containment I can use a nesting link.
bruce