When trying to determine cause-and-affect we cannot forget...
"Correlation does not imply causation."
Perhaps long tossing from his knees had nothing to do with Kimbrel's legendary velocity.
Or perhals Kimbrel throws as hard as does IN SPITE of long tossing from his knees.
That being said...
For me it comes down to the "Principal of Specificity" which states that adaptation is specific to the demands imposed by the training stimulus. If you want to get better at throwing a ball hard off a mound, then practice throwing a ball hard off a mound.
However, taking a page out of strength & conditioning philosophy, we can also facilitate pitching performance by getting better at things that are similar to throwing off a mound -- without actually throwing off a mound.
Long toss certainly has a place in an intelligently-designed throwing program. Perhaps even throwing from the knees has a place in a throwing program.
What training modality, as well as how much and how far and how hard, depends on the individual -- his preferences and goals matched to his needs and (current) abilities -- and the time of year.