It appears that Commerce will always consolidate line items of the same Item ID.  This presents problems in a couple of different ways as described below...

Scenario 1:  Someone creates an order adding more than one item of the same Item ID, but each with different entries for the custom fields.  All of these items will be consolidated to one line item with only the custom fields for the last added item being recorded into the transaction.

Scenario 2: Someone creates an order for more than one item of the same item ID sold in different lengths when units are something other than qty... For example... two lengths of rope sold in inches... one being 3 Inches and another being 1 Inch.  This will simply appear on the sales order or invoice as 4 Inches of rope.  Without the line item distinction, there's noway to show that this is actually two separate pieces of rope.

I would personally suggest that each "Add to Cart" consume its own separate line entry on the Sales Order and Invoice to avoid these problems.