More than 300 rivers drain into Siberia's Lake Baikal, which holds 20 percent of the world's fresh water, more than all the North American Great Lakes combined.
I think it's A too, but I don't understand why you think it's missing 'that of'. What do you think about the following view of the sentence:
More than 300 rivers drain into Siberia's Lake Baikal
[ is the main clause ]
, which holds 20 percent of the world's fresh water
[is a relative clause describing "Siberia's Lake Baikal"]
(which is) more than all the North American Great Lakes (hold) combined.
[is another clause, describing "20 percent of the world's fresh water"]