@justin55 

"As shipping/freight from our ingredient vendors to our co-packer is a direct cost of inventory, wouldn’t those costs still have to be capitalized under GAAP?"  Yes, under GAAP those costs are capitalized.

The IRC provides an exemption to UNICAP rules (IRC Section 263A) for small business taxpayers that meet the gross receipts test as defined in section 448(c).  §1.263A-1(j) is the exemption for small business taxpayers and contains references to section 448(c) and links to §1.448-2(c) that define what the gross receipts test is.  Here is a link to the Regs. Sec.:§1.263A-1