I think a very simple option, such as adding a transfer of items would be great.
We can imagine another organization, a civilian one, collect the items and bring them to your base.
I don't think it's necessary to stop the "exploit" of exceeding base storage with this as it will prevent you from manufacturing and transferring from other bases. We could consider the excess is stored outside the base, and administration refuse you manufacture more items as long as this "unacceptable" state has not been solved...