Those were the ecclesiastical states of the Holy Roman Empire.
Germany as we know it today did not really exist in 1648 - the territories in question were part of the Holy Roman Empire, a highly fragmented feudal polity. Fiefs within the Empire could receive a privilege known as imperial immediacy, whereby they become subject to no other authority except the emperor's. They were de facto independent states despite nominally being imperial vassals.
Immediacy could be granted to a wide range of imperial subjects, most prmoinently hereditary feudal lords, but also cities, knights, and ecclesiastical figures. The video appears to be depicting the ecclesiastical states ruled by the last group, which included bishops or abbots and abbesses. Of course, in reality none of these had anything to do with the Papal States, which refer to territories under the direct and sovereign rule of the Pope.
Most of the ecclesiastical states, especially the abbeys, were tiny; but several prince-bishoprics of the empire were sizeable states. Prior to the Empire's territorial losses and subsequent mediatisation during the French Revolution, there were some 65 ecclesiastical imperial vassals, controlling 12% of its area:
[F]orty-five dynastic princes controlled about eighty per cent of the land and population of the Reich; the sixty-five ecclesiastical rulers, fourteen per cent of the total land area and approximately twelve per cent of the federal population.
Callahan, William J., and David Higgs, eds. Church and Society in Catholic Europe of the Eighteenth Century. Cambridge University Press, 1979.
The ecclesiastical states were thus overshadowed by the dynastic princes in terms of size, population and economic power, not to mention military strength. Nonetheless, they were integral to the imperial constitution and provided prestigious positions for surplus children of the leading dynastic families..
If you examine the following map of Prince-Bishorprics of the Empire, it becomes apparent that this is basically the same territories the video shaded.
Top: Prince-Bishoprics of the Holy Roman Empire, from Wikipedia. Bottom: For comparison, the YouTube video.