The Items Not on Inventory will not help you if the bin content does not exist for that item on that bin.
1. Putting the newly found items on the Whse. Item Journal is correct
2. After the Whse. Phys. Invt. Journal is registered, use the Calc Whse. Adjustment on the Item Journal to put them into the item ledger.
#2 is something you have to do everyday anyway, so we're not creating extra steps when we train our clients on something new.