Let's assume a setup with a static linear molecule with three identical atoms connected by bonds and a single atom, identical to the other three, being shot at the molecule. Let's also assume that everything happens in 1D and can therefore be illustrated by this simple scheme:
(projectile) A -> A-A-A (molecule)
Where the direction of the arrow is the direction of motion of the projectile and the dash signs in the molecule are the bonds between atoms.
Assuming a low-energy, non-relativistic, perfectly elastic collision, the projectile will stop dead in its track while the molecule will be set in motion at 1/3rd of the projectile's speed, as it has 3 times the projectile's mass (conservation of Momentum). Balancing also the equations for the Kinetic Energy easily reveals that 2/3rds of projectile's kinetic energy must have been locked away in internal vibrations of the molecule.
Now, it's easy for us to calculate these numbers by considering the projectile and the molecule as just two separate systems and conveniently attaching a total mass to each. But in reality the universe doesn't group atoms into molecules, does it? Each bond in the setup doesn't "know" about the existence of the other bond and each atom could be said to be unaware of all but the atoms bonded or colliding with it.
In this context, not "knowing" total masses, how does the universe "calculates" that in this case the molecule must store 2/3rds of the projectile kinetic energy into internal vibrations, no more, no less?