A sudden decrease in stiffness can also lead to a sudden increase in stress, which can exceed the strength of the materials. Yes, it can also be a singularity, but if elements with edge lengths larger than the thickness show failure, that is a concern. There is no point in making the elements smaller, since the stress will only increase. Making the elements larger might lower the stress at the centroid, but the unaveraged corner stress may still show failure.
The benefit of shared topology is you know exactly how each element is connected. Bonded contact is acceptable if you can see node-to-node bonds so you know exactly how each element is connected. Use MPC bonds and look at the CE plot.
One benefit of entering the solid adhesive is to determine if there is a shear failure in the adhesive bond. Say you double the thickness of the composite to eliminate the ply failure, how do you know that the load did not cause the adhesive to exceed its shear strength?
The order of the solid elements should match the order of the shell elements that have the composite properties. Aren't they linear?