You have in fact missed something. We use the "not only . . . but" structure when we want to show how a similarity between things intensifies the meaning. For example:
Stephan is not only the ninth most handsome man in the world, but he is also the third most intelligent.
The point of the sentence is that Stephan is a special person in many ways.
In the Lake Baikal example, the author means to contrast the two qualities. It is surprising that the largest lake by volume should be the ninth largest by area. Intuition suggests that the largest lake by volume should also be the largest lake by area.
This is the context in which "only" makes sense.
Yes, it is true that Lake Baikal is the largest in volume. But it is only the ninth largest in area. Isn't that surprising?