tom, not true.
The list is primarily derived from PA state legislature declarations of public highways.
That said, the actual question of navigability is a federal one, not a state one. By current law, such a declaration does not prove that a stream is in fact navigable, i.e. the declaration carries no legal weight on it's own. And on the flip side, a declaration is not necessary for a stream to be, in fact, navigable. There could be streams which are not on this list which are navigable.
Hence the fine print you pointed out. Only a court can decide. Such a declaration by the PA legislature is merely a piece of evidence in favor of navigability. They were declared to be public highways, typically, to protect a commerce route. And the test for navigability is whether it can be a route for commerce....
The list was primarily compiled for gas drillers and mineral rights. If a stream is navigable, it's streambed is owned by the state, and ALWAYS WAS, from the beginning of the Commonwealth. Hence, it was NEVER legitimate private property, despite what any deeds say. And thus it's mineral rights could never have been legitimately separated from surface rights. Hence, the state also owns mineral rights.