No. It very much mattered. The indictment formally documents the charges Ulbricht faced. His lawyer, a relatively well-known defense attorney, was fully aware of his obligation to rebut the allegations in the indictment. Ulbricht is, of course, innocent of charges until proven guilty. The prosecution produced what appears to be very compelling evidence. The defense produced something much less compelling.
A variety of things that aren't findings of fact at criminal trials can, unfortunately, be material to the sentencing phase of a trial. The murder-for-hire scheme isn't one of those things: it was an explicit component of a criminal charge that Ulbricht was convicted of, supported by evidence, provided to the Ulbricht defense during the earliest phases of the trial.