You're cutting out the most important parts:
> The Court agrees with the government that applicable Ninth Circuit authority precludes the defendant’s success on his motion. SEI’s identification of the defendant’s IP address because of his use of the Tor network did not constitute a search subject to Fourth Amendment scrutiny. The Court reaches this conclusion primarily upon reliance on United States v. Forrester, 512 F.2d 500 (9th Cir. 2007). In Forrester, the court clearly enunciated that: “Internet users have no expectation of privacy in ...the IP address of the websites they visit because they should know that this information is provided to and used by Internet service providers for the specific purpose of directing the routing of information.” Id. at 510.
> In the instant case, it is the Court’s understanding that in order for a prospective user to use the Tor network they must disclose information, including their IP addresses, to unknown individuals running Tor nodes, so that their communications can be directed toward their destinations. Under such a system, an individual would necessarily be disclosing his identifying information to complete strangers. Again, according to the parties’ submissions, such a submission is made despite the understanding communicated by the Tor Project that the Tor network has vulnerabilities and that users might not remain anonymous. Under these circumstances Tor users clearly lack a reasonable expectation of privacy in their IP addresses while using the Tor network. In other words, they are taking a significant gamble on any real expectation of privacy under these circumstances.
> [...]
> The evidence before this Court indicates that SEI obtained the defendant’s IP address while he was using the Tor network and SEI was operating nodes on that network, and not by any access to his computer.
SEI got the IP addresses because the Defendant's computer communicated that information to SEI.
You can imagine that the briefing went something like this:
Government: there is no expectation of privacy because connecting to Tor involves giving out your IP address to random people on the Internet.
Defendant: but the purpose of Tor is to hide your IP address from anyone that might matter.
Government: well obviously that didn't work because we figured out his IP address.
The point of vulnerabilities isn't the basis for the Court's opinion--it's just a rebuttal to the idea that Tor is supposed to keep your IP address secret even though it necessarily involves giving it to at least some untrusted nodes.