US Topo

US Topo maps and the maps of the Historical Topographic Map Collection (HTMC) can be downloaded free of charge, in PDF fo
Traditional national mapping programs gathered data from primary sources, including direct field observation. Such maps were compiled, drawn, and edited by hand.
Yes, it is possible to convert GeoPDF to GeoTIFF using both commercial and open source software.
The original USGS 7.5-minute topographic map series (1945-1992) included feature classes that are not yet shown on US Topo maps.
There are different answers to this question for different products.
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 except the US national boundary.
Possible explanations and solutions include: 
The USGS no longer has mission or funding to collect and maintain data for roads and other transportation features.