It applies perfectly. The 49° N section of the border was set in the Treaty of 1818 [1], at which point all affected regions were still populated by native americans.

You can see on this territorial expansion map [2] of the United States, how the lay of the border differs between the first-settled east and the later-settled west.

[1] https://en.wikipedia.org/wiki/Treaty_of_1818

[2] https://upload.wikimedia.org/wikipedia/commons/2/29/UnitedSt...