Example:
A player has a chest open. A plugin needs to know whether the player clicks an item in their inventory or on the chest. Both items are in their equivalent inventory's slot 0. Currently there is no way, unless you know for absolutely certain that the two items are different or what they both are, to know which inventory the event occurred in. InventoryType will yield CHEST for both areas and the slot is identically numbered in both areas.

This could be resolved through the introduction of a new API that itself reports which section of the inventory (For the example above, CombinedInventorySection.PLAYER would be an easily checked solution for problems like the example above).