Reality Winner may not have been "in custody" when she made her confession. If so, (a) the FBI agents were not required to give a Miranda warning and (b) the confession very likely is admissible. The outcome suggests that the prosecutor persuaded the judge that the circumstances did not require the warning. It appears Ms. Winner forgot or did not know the cardinal rule for dealing with law enforcement officials in any dicey situation: say nothing without legal advice beyond what is required to establish or confirm identity.
As for the prison suit, there are a few plausible explanations, one of them that the defendant's ploy irritated the prosecutor, who might have thought her better strategy would be to negotiate a guilty plea and two or three years in custody with some credit for time served. The information released, while classified, did not come as a great surprise to most, and revealed very little in the way of sources and methods.
In my opinion, there is a better case to be made over a delay of more than a year and a half between arrest and trial, which falls a good deal short of the sixth amendment requirement in what seems a fairly uncomplicated case.