A reader writes:

James Fallows wrote an article about the "throwing like a girl" issue back in the '90s, and it came to a very different conclusion than the pieces you cited. In Fallows' analysis, a great deal of the difference is practice and competition. He updated the piece last year for a discussion of The Freak's throwing motion (not sure if you follow Giants baseball, but Tim Lincecum is a slip of a man who achieves a blistering fastball through an extraordinary chaining of potential energy through his body).

Another offers a more creative theory:

The most persuasive and thorough scholarly analysis of the phenomenon of "throwing like a girl" comes from Iris Young, who argues (contra Maurice Merleau-Ponty's embodied phenomenology) that the limited arm motion that results in "throwing like a girl" is the result of internalized cultural imperatives that women hold their limbs protectively close to their bodies, as a way to prevent rape and other forms of gendered violence.  Women and girls throw the ball in a particular way for the same reasons they sit with their legs closed, walk with a limited arm movement, and carry things close to their bodies – because full extension of limbs opens the body, rendering it physically vulnerable.  

Put another way, "throwing like a boy" is part of male privilege of being able to possess a body and move it in space without fearing that is boundaries will be breached.  And "throwing like a girl" is an embodied manifestation of the psychological and practical effects of pervasive male violence against women.   Which is why the phenomenon of "throwing like a girl" is present across a broad spectrum of geographic and historical locations.  Wherever there is male-domination and/or pervasive violence against women, you will find "throwing like a girl."

For theory geeks, Young was critiquing Merleau-Ponty's Phenomenology of Perception, which posits that the human body is the starting point of selfhood, that perception is always measured against biological centeredness and the simultaneous physical limits of the body mediated by its ability to extend itself into the world (by throwing a ball, for example).  Young's point is that Merleau-Ponty's phenomenology assumes universal subjectivity, ignoring the fact that women experienced themselves simultaneously as subjects (able to extend themselves by throwing a ball) and objects (often of male violence, which causes them to hold their limbs close to their bodies to protect themselves).

Another is more practical:

What the "practice and competition" explanation ignores is the effect of height. Height is an advantage in throwing. Men 6’3” and over represent 3.5% of the population but 50% of major league baseball pitchers. The average male height in the US is between 5'9" and 5'10". On the list of the 100 pitchers with the most all-time wins there is only one who is less than 5’10, Eddie Cicotte standing 5'9" with 208 wins. He’s 98th on the list. The leader, Cy Young, had 517 wins and stood 6’2".

No amount of practice and competition makes you grow to be 6’2”.