I might be mistaken, but it seems to me this paper discusses unintended ways of obtaining the IP addresses of clients involved in transactions on the core Bitcoin network.
Tor was mentioned only insofar as it might be one's first thought of how to mitigate this risk, yet Bitcoin over Tor has its own problems that prevent this from being effective.
But the primary "issues" mentioned in the paper are regarding a Bitcoin node in default operation, no?

"In their new study, researchers at the Laboratory of Algorithmics, Cryptology and Security of the University of Luxembourg have shown that Bitcoin does not protect user's IP address and that it can be linked to the user's transactions in real-time."

"The basic idea behind these findings is that Bitcoin entry nodes, to which the user's computer connects in order to make a transaction, form a unique identifier for the duration of user's session. This unique pattern can be linked to a user's IP address. Moreover, transactions made during one session, even those made via unrelated pseudonyms, can be linked together. With this method, hackers can reveal up to 60 percent of the IP addresses behind the transactions made over the Bitcoin network."

"'This Bitcoin network analysis combined with previous research on transaction flows shows that the level of anonymity in the Bitcoin network is quite low,' explains Dr. Alex Biryukov."

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