They're not overlooking this, they're criticizing it.
Suppose you have to prove that someone occupied "a position of organizer, a supervisory position, or any other position of management" so you introduce several pieces of evidence to try to prove it, one of them is some sketchy murder for hire allegations from a low-credibility source. The jury then convicts on the conspiracy charge without indicating whether they believed the murder for hire claim was proved beyond a reasonable doubt.
Should you now use the murder for hire claim to determine sentencing for the conspiracy charge? No, that's crazy, it's a much more serious crime and they should have to charge and prove that as a separate count if they want it to affect the penalty.
The source is a bunch of chat records from Ulbricht's seized laptop. There's a fairly detailed description of the evidence here [1].
[1] https://s3.amazonaws.com/s3.documentcloud.org/documents/1391...
In particular, the chat logs allegedly contain multiple separate instances of murder for hire, but then the claim that Ulbricht had already been sentenced to life without parole as the reason these claims were never prosecuted doesn't make sense, because a conspiracy to commit murder has multiple parties, so where are the murder prosecutions of these alleged contract killers and co-conspirators?