I will just chime in to say I'm not sure there's any good answer to this that I have seen. If I were to speculate, I would suggest that this was a product of desperation on behalf of the interrogator, which fed into a desperation to learn more information from his superiors. It is of note that the Japanese had competent scientists who knew quite a bit about the properties of fission and would have immediately seen that his explanation of how the bomb worked was just made up nonsense. As actually happened.

One thing when dealing with strange intelligence assessment is to remember that they aren't being dictated by national policy (it's not "Japan" that interrogated him), but by the individuals who are doing the interrogation. So you can easily have weird forces warping them because, say, the interrogator has a weird notion, or desperately needs to give something to his bosses to avoid being suspected, or whatever. This is why intelligence is usually read with a grain of salt, because there is a big gap between "what your informant/prisoner tells you" and "what is true."

One could, of course, imagine that someone who was coming in from the island of Tinian might have some clue about this — maybe he'd seen the atomic bombs being loaded up, and would know if there were a lot of them around. There is no way for them to have known how heavily compartmentalized the atomic weapons work was, even at a place like Tinian, nor how effective such compartmentalization might have been.

Separately it has never been clear to me that anyone actually took anything he said that seriously. They did a cursory evaluation of it, concluded his details were nonsense, and I don't think it had that much of an influence on their later thinking. The US also tracked down every weird rumor it heard about, too, just to be sure.