I don't think he does. He's reading the code directly.
Neo surprises him at the console in the middle of the night. He jumps, then quickly hides what he was doing - from which I always understood that he was in the middle of his conversation with Agent Smith. When Neo finally leaves, we see him in the restaurant, presumably finishing the interrupted conversation from before - but, as you say, there's no evidence that he was jacked in or that he had an operator.
I think that the continuation is just the same as before: he's interacting via the code, and he's so used to it that, as he says to Neo, he just sees "blonde, brunette, redhead..." - and, he tastes the steak in exactly the same way.