Note that in the video the "RETARD" callout is heard which is what you would expect to hear on a normal landing. After a quick look in the FCOM I can’t find anything to say that having the gear up would stop this call, it seems to be simply triggered by the RA. As per Pavlov's dogs, the crew retard the thrust levers expecting a normal touchdown believing they are back in the ballpark.
But where do you draw the line for ATC intervention?
This crew were in excess of normal parameters by about double, ATC should have the authority to discontinue an approach when it exceedes normal plus a certain percentage, unless a MAYDAY call has been made. I don't want to be told to go around because I had VS - 1100 fpm briefly at 1000' but if a safe landing is in doubt, it's a further safety layer. Complying with an ATC instruction enables the crew to save face, anyone who has flown in Asian knows how important that is, and it cuts through confusion and tunnel vision.
In aircraft carrier operations, the Landing Signals Officer has full authority to "Wave Off" any approaching aircraft if it deviates from set parameters. I'm not suggesting this is needed at civil airports, but safety might be improved if ATC were to enforce a "gate" on arriving aircraft which if not met would result in an immediate instruction to go-around.