FAR 52.211-6(b) clearly identifies what the contractor MUST do to be considered for award.  In this case, the solicitation provided an attachment with the specifications for the NOX35 and the HALO-LR.  In your question, you clearly state the “Alternate Product awarded did not fit exact description of brand name product but the USDA Program making the purchase said the lower cost alternate product was suitable.”

Based on the information provided and your statement above, I would tend to side with the vendor’s perspective that award of the alternate is unfair.  I strongly recommend the Contracting Officer should consult with Legal and Policy advisors due to a potential protest.