Sorry for chiming in late. I'm brand new here.
I think it is important to differentiate correlation and causation as it relates to the flexibility and throwing velocity...
Flexibility may be associated with throwing velocity (<--- correlation) but that doesn't necessarily mean that increasing flexibility increases velocity (<--- causation). Do you see the difference?
There is no denying that the arm must achieve some pretty extreme postures during the throwing motion but these are likely more a by-product of throwing hard rather than a pre-requisite to throwing hard.
As far as increasing shoulder mobility, while some of the most flexible people in the world stretch on a daily basis (causation) the mechanisms are poorly understood and not well agreed upon. Joint mobility is the net-result of a complex interaction of many neurophysiological factors that can be manipulated in many ways other than traditional flexibility training.
My advice would be: if you are going to stretch, approach it in a very progressive manner. Yanking your arm into weird, uncomfortable, painful positions or going too far too soon is counterproductive to your goals.