USS GAMBIER BAY CONSTRUCTION PUZZLE

I recently purchased a Yankee Model Works USS Gambier Bay model.  I have many years of experience with static and RC modeling, but this is my first experience with resin models. Has anyone built this model or is familiar with its construction?  I am puzzled by a large section of flash (1/4 inch thick) at the end of each half of the carrier deck assembly.  I am not certain it should be removed or whether it is meant to leave a recessed opening between the two halves for other parts to sit inside of (instructions are not clear).  Can anyone help?