It appears that the import (and export) assumes that all category names throughout the hierarchy are unique.
For product sites, this assumption seems too limiting, and in my view...flawed.
For example, we group products by their type into categories for presentation on the front-end.
One product type we offer is "Flags", another is "Windless Flags". The intended use, cost and prospective customers are unique, so this type of grouping is needed.
Within each of these categories are child categories for the applicable industries as shown below:
Flags
-> Automotive Repair
-> Car Sales
-> Food Service
Windless Flags
-> Automotive Repair
-> Car Sales
-> Food Service
The export does not create a fully-qualified path in the hierarchy. For example, the categories column exported might contain "Car Sales", which could apply to either parent, "Flags" or "Windless Flags".
When I assign categories, export, then import, all flags that were in "Windless Flags \ Car Sales" are moved to "Flags \ Car Sales".
To the point, it would seem that the export and import should reference a fully-qualified category, rather than assume that all children within the category hierarchy are unique.