If the aircraft was doing 236 kts at 2000' that suggests that the gear would have been down if it had been selected down, as the speed was now below the lockout speed. The tower controller has a very good view of the runway and would/should have been watching the aircraft to confirm its arrival and hand him over to ground frequency once vacated. He doesn't notice that the wheels aren't down, it isn't his job to check and everyone else manages to do it correctly. Possibly the view is distorted by the shimmering heat, dirty windows or fasting for the last nine hours.
He becomes concerned at the aircraft's excessive speed along the runway and at some stage realises that the landing gear is retracted. He assumes that there is a problem with the undercarriage and that the crew are aware of it but neglected to tell him, hence his query about carrying out a belly landing.
The primary cause of this accident was continuing the badly unstabilised approach instead of going around, and the final decision to continue appears to have been made when they informed the controller that they were established and could make it. The CVR should reveal if there was any mention of going around after this or if they tunnel fixated on landing the aircraft.
The events leading up to this, such as how they got into that position in the first place and the exact errors and sequence in which they happened should be revealed by the investigators.