There may be a benchmark out there where std::set can beat std::unordered_set, but you'll be really hard pressed to find it
Java uses balanced trees instead of linked list in their chained-hashtable implementation, if I recall correctly.
std::unordered_set has some very difficult to reason about worst case scenarios that must factor in both the size of the collection and the hash function. Unless you are very careful about the type of hashing you use, you can easily be vulnerable to DDOS attacks that scale on the order of O(k * n) for key size k and container size n.
I could go on, but it's very much detracting from the point of the paper to argue about the data structure choice when the paper isn't on this topic at all or trying to analyze any particular application to begin with.