The allowance is used to purchase the GFP. The material is already purchased with this allowance. However, your question is focused on shipping costs. The contract should contain a CR CLIN for shipping of the excess material.  If the Government allowance paid for the materials, the Government shouldn't have to pay for the material twice. 

See for further research FAR 4.10 Uniform Use of Line Item Numbers.

More specific instruction for DoD are provided in  PGI 204.71 -UNIFORM CONTRACT LINE ITEM NUMBERING SYSTEM