Acumatica assumes that inventory transactions for lot/serial trace items will be at the exact quantity ordered.
When multiple lots are required to build the actual quantity in a line, the quantities must be entered twice, once, by lot in the Allocations pop-up and once for the total in the grid line.
Acumatica should take the total of the quantities in the Allocations pop-up and populate the actual qty in the transaction. It does this for over-transactions. It should do this for under transactions too.