How could the FRCP work otherwise? They're in effect saying: if the evidence pertinent to a crime is online, and is either (a) on Tor or some other service where we don't know precisely where it is, or (b) on a botnet or some other environment where it's spread across 100 different jurisdictions, a judge can issue a warrant to obtain that evidence.
Judges can already issue warrants to obtain electronic evidence in, I think, exactly the fashion EFF describes here. The limitation they have today is procedural: they can only issue those warrants in their own court district.
But if you don't know the right court district, or a search would effectively require you to get warrants in every district, procedural rules make it hard to get a warrant today. That seems... stupid. The fact that evidence pertinent to a criminal case is on a Tor hidden service shouldn't make it inaccessible to the courts.