I am no expert on baseball bats, but I can give you some information about the difference between the molecular structure of aluminum alloy, and wood. How this has anything to do with the performance of the bat is pure speculation, and hence NOT science.
Wood is made of organic molecules (based on carbon and hydrogen and some oxygen). The metal bat is an alloy of several elements, mostly aluminum with small amounts of silicon, manganese and trace amounts of other elements.
In the wooden bat, the major molecular component is cellulose. You can picture cellulose as a tangled long chain of millions of six-sided carbon rings connected by oxygen atoms, with hydrogens hanging off all the spare places. Holding all this cellulose together is a kind of glue called lignin, which is another kind of organic carbon chain. The wood bat is organic. It has no crystal structure, but a complex structure of intertwining and embedded organic molecules.
The aluminum bat would be crystalline in structure, and somewhat amorphous, meaning that the lattice or the matrix of the crystal would not be perfect as in a diamond or other gem. The way the crystal behaves to transfer the energy to the ball is very complex. I found a site that gives basic information about steel which would be very similar to aluminum at How Things Work. Read the sections on Strain and Stress and Plastic Deformation, pages 2 and 3.
To make an aluminum bat, a tube of aluminum is drawn to redistribute the walls with the desired weight. After tempering (which is a controlled heating and cooling process that affects the strain, stress and deformation behaviour of the finished bat), the bat is tapered to the proper dimensions. Cleaning treatments and heat treatments are performed on each bat. The bats are polished and anodized (which is a method of applying a surface finish using electricity).