The emissions reporting thresholds are in the Air Emissions Reporting Rule (AERR), 40 CFR Part 51, Subpart A, Appendix A, Table 1, which require state/local air agencies to report emissions as point sources for facilities that meet or exceed these emissions thresholds.
The AERR requires states/locals to report to EPA, and the state/local rules require facilities to report to them.
While some states/locals use the same thresholds as the AERR, other states have lower limits and also require Hazardous Air Pollutants to be reported. Usually, the states/locals also send in these smaller point sources voluntarily and they are included in the NEI as well. A select few tribes also report point sources.
When the emissions are not included in the National Emissions Inventory as point sources, they are captured as nonpoint sources as a county total for emissions processes, called source classification codes (SCCs).