A.o.A
I was also facing severe vibrations/knocking alike in my vitz 2010 model when speed was between 20-60 km/h. Below and after this speed, engine was smooth. For about a year, i checked with different mechanics but no solution was found. It felt to me that the engine had problem. But after tuning and changing somethings, problem was still there as it is. (I did not rebuilt or swapped engine)
Recently, a mechanic asked me to change mount/foundation of engines. I decided to change mount one by one. First i changed the timing belt mount (the big one on top left side), not much helpful. Then, i changed the 2nd mount which is below battery and it worked.
Now the engine is smooth throughout 0 to 140 km/h.
I am not sure if that is your case, but it is worth a try. You can try changing mount one by one and return it back if it does not work. I hope this helps.