I can answer this based on classical mechanics and thermodynamics. Someone else may have a quantum mechanics perspective.
The baseball is a collection of atoms and molecules. The velocity of the baseball is the velocity of the center of mass of the collection with respect to an external (to the baseball) frame of reference (say, the ball field). As such, the collection of atoms has a macroscopic velocity and kinetic energy.
At the microscopic level, the baseball molecules have random translational and rotational velocities that constitute the internal kinetic energy of the baseball (the other component of its internal energy being microscopic potential energy).
The microscopic random velocities of the atoms and molecules of the baseball (the baseballs internal kinetic energy) are not effected by the macroscopic velocity of the collection of atoms and molecules (the baseball's external kinetic energy). The sum of the internal kinetic and external kinetic energies constitute the total kinetic energy of the baseball.
Hope this helps.