The main problem is that they are just a blank item until they enter a player's inventory, at which point they become a container item and are populated with the loot. After that, they can be given to a turtle which can, I am led to believe, call turtle.place() with a chest in front of it, and the contents will go into the chest just like if a player had right-clicked on the chest with the spoil bag. Any item that can simulate a right-click with an item will do, but the only other one that I am aware of is Tool Dynamism. There might be something in Engineer's Toolbox that can do it.
Spoil bags that go directly into my AE system from my mob farm all stack up with each other, as they are identical items with no NBT data. Once they've been into my inventory, they appear as different non-stacking items in AE.