Short version. It's not about ball position so much as it is about arm to torso position, and the lack of angular body lean, real meaninful weighted rear footplant to build up potential energy. Followed by conversion to kinetic energy when the QB shifts his weight forward (through forward angular torso lean, transferring his weight to the front foot, and strong arm follow through). Madden does NOT animate the conversion of potential to kinetic energy well when the QB throws the ball.
In other words, it lacks the "physics" to execute a real life in game pass.
Long version. It's not so much about the relative ball position, and the direction it's pointed towards. It's about the angle of the arm relative to the QB's upper and lower body. Look at all the posted QB throwing motions just in this thread. The torso has a angular lean. Think about throwing a deep, deep pass. It requires stepping up in the pocket, leaning your torso backwards, transferring your body weight to the back foot to build up potential energy.
This potential energy gets converted to kinetic energy when the ball is released. When the QB steps forward, plants his front foot, changing his torso position from an angular backwards lean to an angular forward lean is what's missing from Madden's QB throwing motion. Look at real life footage or (apologies ahead of time) APF2K8' QB throwing motion.
Madden's QB animates with the torso essentially completely upright with no build up of potential energy through body lean. Throw a football with the same motion in Madden and you won't get far. It's literally all arm strength in Madden.