In 2016, a National Academies of Sciences, Engineering, and Medicine advisory committee proposed omics technologies as one possible adequate response to the regulatory challenges posed by gene editing and synthetic biology. This paper presents a set of questions that would need to be answered to integrate omics experiments and data into crop regulatory systems. These questions concern both experimental practice and how omics-experimental and regulatory systems intersect. We anticipate that the chosen answers to these questions will impact the scientific validity, regulatory burden, and usefulness for forecasting risk in nuanced ways. In doing so, we conclude that the integration of omics technologies into regulatory systems poses an array of more-than-technical dilemmas whose management will require cross-sector collaboration and innovative approaches to socio-technical decision-making.