Boundaries are an ongoing issue for the US Topo project due to the lack of national GIS datasets suitable for general-purpose, 1:24,000 scale maps. The earliest US Topo maps (2009-2010) showed no boundaries other than the U.S. national boundary. In 2011, state and county boundaries were added using TIGER data from the U.S. Census Bureau. Federal land boundaries are being added as the relevant agencies are able to provide data. U.S. Forest Service (USFS) areas were added in 2011. National Park Service lands, Fish and Wildlife Service lands, and military reservations were added in 2013. We hope to add federal wilderness areas in 2018.
Unlike traditional hand-drawn maps, boundaries on US Topo maps don't always align as one would expect because different sources have not yet reconciled their data. This leads to some odd visual effects, such as the southern boundary of Texas (from the Census Bureau) not perfectly matching the U.S.-Mexico boundary (from the International Boundary and Water Commission, or IBWC). In this particular case, the Census Bureau has committed to adjusting their data to match the IBWC data. Other cases, such as adjacent National Forests and National Parks, are more difficult but will be resolved over time by the appropriate agencies.
An important detail to keep in mind is that USGS maps are general reference publications and are never legally authoritative sources of boundary information.