There are cases where a subcategory gets repeated multiple times, such as "Parts & Accessories" or "Other" being present within various top-level categories.

The problem is that when importing products, only the individual category name is referenced, with no way to indicate who it's parent is.

What I would suggest is to enable a subcategory to be referenced by one or more parents such as "Couches, Couches:Love Seat, Couches:Full Length"

In this way, the store would properly categorize the imported products.