What I'd like to know is how they seized it. It requires they find his private key - either Ulbricht made serious blunders when storing his private key, or (paranoid) the FBI had some techniques to get it that we wouldn't expect.
"X years in jail if you give us the keys, X^2 if you don't" works nicely, I'd imagine. Plea agreements are a very, very powerful - and potentially abusive - tool.
Don't they usually make that public?
Sometimes it comes out later. In this case, it may be to their benefit to sow a little doubt over how they obtained it.
We also know that they waited until he entered some keys on his laptop before they seized him. The likelihood it was these keys is probably low, but still should be considered.
He blundered or he caved. We only have evidence of past blunders so that is the best guess.
I have to assume it was traded as part of a deal with the prosecution. He made plenty of blunders, but if he had legitimately messed up with the encryption or storage of these coins it would make much more sense that they would have found the hole and seized them right from the start.