From the Help files (really)

Defining the Hierarchy of Costs

Note For standard and average cost items in Purchase Order Entry, Receipt of Goods Entry, Return of Goods Entry (no purchase order specified), the cost hierarchy for each valuation method is followed. In Material Requisition Issue Entry (one-step) and material requisitions entered in Purchase Order Entry, the cost hierarchy for each valuation method is followed.

Hierarchy of Costs for Purchase Order Entry, Receipt of Goods Entry, Return of Goods Entry (one-step), Material Requisition Issue Entry (with a Purchase Order number assigned), and Auto Reorder Selection:

The Vendor’s price level is used; however, if a vendor’s price level does not exist, then the primary vendor's last cost specified in the Item Vendors Maintenance window is used. If this value is zero, the item's last cost is used. If the last cost is zero, then the valuation methods listed below are used.

Hierarchy of Costs for Auto Generate from Sales Orders:

In Auto Generate from Sales Orders, when Costing Hierarchy or Last Unit Cost is selected in the Update Unit Cost With field, the primary vendor's last cost is used from the Item Vendors Maintenance window. When Standard Unit Cost is selected at the Update Unit Cost With field, the item's standard cost is used. When Average Unit Cost is selected in the Update Unit Cost With field, the item's average cost is used. If any of the costs are zero for the above selections, the unit cost used follows the cost hierarchy based on the valuation methods listed below.

Can the cost hierarchy be overridden with a script to always use the CI_Item last cost?

I'm going to say maybe.   I say that because sometimes what seems simple has something that blocks it from happening in the program logic.

Of course if your valuation is FIFO it should be last cost anyway.

I am going to say no because the cost is not part of the file for Serial, Lot, FIFO items.

Anywhere you can type in a value to override manually, can be scripted to override.  It won't be easy, depending on what you want to do, and certain data changes will recalculate the field (so you'll need to be vigilant in your script setup).

I agree with BL on a  return of goods  That cost must come from the inventory costing records just as it would during a sale.

A purchase order entry would use the hierarchy as set out previously.  The default will come from the hierarchy not the inventory costing records so you should be able to override either manually or via a script.

Receipt of goods I believe gets its info from the referenced purchase order and once again should be overrideable.. 

No matter what, you just have to try it in a script and see what falls out.

Agreed with returns.  There is no control of costing there (which makes reversing a mistaken RoG a bit of a pain).