According to the court documents that detail the changes:
"...a magistrate judge with authority in any district where activities related to a crime may have occurred has authority to issue a warrant to use remote access to search electronic storage media and to seize or copy electronically stored information located within or outside that district if: (A) the district where the media or information is located has been concealed through technological means; or (B) in an investigation of a violation of 18 U.S.C. § 1030(a)(5), the media are protected computers that have been damaged without authorization and are located in five or more districts."
By "concealed through technological means," the Supreme Court is saying that a warrant will be granted if a suspect uses Tor or any other tool to remain anonymous.
DOJ spokesperson Peter Carr told Motherboard:
"Criminals now have ready access to sophisticated anonymizing technologies to conceal their identity while they engage in crime over the Internet, and the use of remote searches is often the only mechanism available to law enforcement to identify and apprehend them.
This amendment ensures that courts can be asked to review warrant applications in situations where is it currently unclear what judge has that authority. The amendment makes explicit that it does not change the traditional rules governing probable cause and notice."
Just a few days ago, the court threw out evidence that the feds got through hacking the members of a child porn service on the Tor network. The judge explained that they violated Rule 41's territorial restrictions. This change would prevent something like that from happening. However, as Google's Legal Director Richard Salgado said, it could also "have profound implications for the privacy rights and security interests of everyone who uses the Internet."
The Congress has until December 1st to reject or make more changes to Rule 41, after which the amended version will take effect.