I own a Fly. The dropouts are fine for me. A Fly is designed as function first. Just like a Calfee's lower bottle bosses on the seat tube have a reason I'm sure this design has a reason as well. In a like manner the bottom bracket and head tube do not use ti like a Tetra. The aluminum is lighter and Craig knows now that his isolation technique from the carbon works great. He used aluminum because he could make it lighter. A Fly's "function" is light and stiff.
The only thing I really noticed is the serial number is now on the outside of the dropout. This reinforces the hypotheis that there is a reason for the inside design.