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I'm wondering why they ended up using BSP as a data structure for boolean mesh operations. Is there an advantage over Octrees I'm not aware of in this case?

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Aparently, yes: http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8659.2009....

Just for the record: The original paper in which they found that merging the trees of binary space partition yields set operations: http://www.cse.yorku.ca/~amana/research/bsptSetOp.pdf

For the use case of boolean mesh ops the majority of the work is polygon splitting and clipping, something BSP trees excel at.

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