This is the critical point as the judge notes. The FBI isn't proving that he owns it yet, just submitting it as evidence. The judge can't rule based on the fact that the FBI will eventually prove that Ulbrircht. At this point it's just a server that the FBI found something on they're planning on using in the trial. Combine that with the fact that the fourth only protects your own property from search and there's nothing the judge could really do.
There's some additional oddness around if the sworn affidavit would could be used to prove he owned the server later in the trial. It sounds like he could plead the 5th and the affidavit wouldn't hurt him but I'm not sure.
> “Defendant could have established such a personal privacy interest by submitting a sworn statement that could not be offered against him at trial as evidence of his guilt (though it could be used to impeach him should he take the witness stand),”
It's very similar to the reason judges have had to reject legal challenges to the NSA spying apparatus, the defendants couldn't show that they had standing, i.e. they were affected by the law.
In short his lawyers screwed up by failing to prove he had any standing to challenge the server as evidence in the first place. Providing this proof would give an unknown amount of damage to the prosecution but the contents of the server would not have been admissible at least.
So in short his lawyers fucked up
But don't they need to do this at some point in order to get a conviction - if this server is that used to run Silk Road and they want to prove that he ran the Silk Road then it seems like a necessary step. At the point of them making this claim surely the judge has to say "if this evidence proves the defendant owned the server then you've infringed his rights under the Fourth Amendment and the evidence must be discounted"?
Yes, a server they potentially broke into and violated someone's privacy over. Why does it have to be more complicated than that?
In fact, someone at the FBI should be charged with some sort of illegal-seizure crime, or violation of privacy crime. Whatever it's called these days by the lawyer-priesthood.
But that pretty much exactly that FBI and other agencies are doing right now in the Internet. And this ruling puts a legal precedent footing under such behavior.
In the US, trial courts find rulings of fact, and appellate courts find rulings of law. Only the latter create precedents.