They agreed, the judge didn't sign off so he's now plead not guilty. Which, that was going to be one incredible deal if he'd been able to walk out with that.
It's the same deal, they just specified at the judge's behest that the agreement only covers the specific charges the agreement was about.
Sure, blanket immunity for all crimes forever would be an incredible deal, but seems like that was never the intended deal considering how fast they just added whatever specific language the judge wanted to the deal and everyone was happy.