Why would a pilot on final to a towered airport not speak up when ATC clears another aircraft to land on the same runway, without mentioning them?
why wouldn't the pilot of '1DA speak up?


The simple answer is that you are not trained to "speak up" at a towered airport, you are trained to follow instructions from the tower and there is an assumption the tower will provide separation and appropriate clearances. As an ultimate fall back you are always supposed to "see and avoid". 

For the official report you should reference the NTSB report but if you listen to the ATC audio in the linked video as well as their explanation of the link the pilots had no reason to think there was an issue and the clearances given were rushed but explicit. As I note above AOPA also notes 


  "it is a pilots responsibility to visually confirm final approach"  


You can also hear that the pilot of '4SR was giving confusing instructions about base extension and clearance to land. The pilots was not incorrect in his approach actions but made a critical go-around error and may have been a low altitude, dirty config, stall.    

Ultimately the lower aircraft on approach had the right of way so '1DA had no reason to speak up as they were in the right. AOPA states that the pilots may have thought "he was overtaking the aircraft from above" which is incorrect, or at least procedurally incorrect as '4SR would have had to yield to '1DA anyway. 

In the end the controller should have simply issued 


  '4SR Go Around


Any time, you as a pilot hear that you should build the habit to just go around. As PIC you can ALWAYS execute a go around, controllers should be prepared for it and more importantly you as the PIC should be prepared for it.