IANAL

Usually judges don't issue such extreme orders only because of the fact that they don't want to be hammered on appeal.

Now this one is different. I have 2 theories: either the judge thinks the mandatory negative inference is not needed because there's a good chance the jury will do that anyway, or the judge is gonna advise the government to make this a separate case.

It honestly doesn't sound to me like he's just saying one thing and doing the other. He sounds rightly agitated and usually agitated judges will give you a low blow sooner or later if you fuck around.