The pilots wouldn't get that close to the earth without audible warnings that they neglected to "follow the checklist" and put the gear down.

If there was a landing gear problem, they would have known about that, and so would the controller (along with a large percentage of the world).

What's impossible is the pilots getting the aircraft to the point of landing, without realizing that anything is wrong and the controller noticing that they "forgot" to put the gear down and pointing it out. If the gear wasn't down, for whatever reason, the pilots would have been well aware of it and it would have been them bringing it to the attention of the controller.

Based upon what was written and what wasn't otherwise reported anywhere else, everything was normal, the controller thought he didn't see landing gear and called for the plane to go around. When he realized the gear was, in fact, down (his error) he amended his instructions and cleared the plane to land.