There are specific circumstances where putting someone on their stomach can be safe and helpful. However, pretty much every police training manual and instructor in the country states that once you have cuffs on a suspect, you are to immediately put them in a neutral (e.g. sitting) or standing position. This is for the safety of the suspect. This was a hard lesson learned after people with all sorts of medical conditions died after being left laying face-down while handcuffed.
In exactly zero situations are police instructed to place a knee on someone's neck after handcuffs are on. In 99% of cases, police are told to use a knee on the back of the shoulder DURING arrest while gaining control over the suspect. A knee on the neck gives ZERO additional mechanical advantage over having one on the neck, but has HUGE risks from a medical perspective. Regardless of where the knee was placed during arrest, it comes OFF the suspect once they are in handcuffs and the suspect is placed into a medically safe position.
Why? So they don't die in custody. Talk to police training instructors before posting stuff like this. They'll explain it better than I can.
He was having trouble breathing and stated that even BEFORE he was on the ground. Is the article wrong about proning helping people who are having trouble breathing?