The US Food and Drug Administration (FDA) and the US Department of Agriculture (USDA) have issued documents about genetically modified (GM) animals and plants for public comment (Nature 546, 327–328, 2017). Discussions are ongoing, so your implication that these have “come to opposite conclusions” seems premature.

You note that the agencies are confined by agency-specific statutes, but do not fully acknowledge the differences in the statutes' scope and focus. For example, the FDA has to evaluate the effects of intentionally altered genomic DNA on the health of the modified animal as well as any risk to food safety, whereas the USDA needs to focus on plant health. In addition, the FDA oversees the safety of genetically engineered plants as food for humans and animals, as described in the Coordinated Framework for the Regulation of Biotechnology.