To what FAA office or personnel should one direct an inquiry about the reasons behind the airspace design at a particular airport?
By reading your linked FAA Order and finding references for responsible offices and a little follow-on search, I found this link to the Office of Mission Support within the Air Traffic Organization.  

Airspace analysis appears to be within their purview:  


  Mission Support Services oversees the Air Traffic Organization’s
  activities in:  
  
  
  Aeronautical Information Manual (PDF)
  Aeronautical Information Services
  Air Traffic Organization Environmental Reviews
  Air Traffic Procedures Advisory Committee (ATPAC)
  Instrument flight procedures production/charting
  Metroplex
  New York/New Jersey/Philadelphia Airspace Redesign
  Obstruction Evaluation/Airport Airspace Analysis (OE/AAA)
  Performance-Based Navigation (PBN) Implementation And Usage Dashboard
  Pilot Web
  


They provide the following contact information:  


  Address
  FAA National Headquarters
  1028 - 10A
  800 Independence Ave., SW
  Washington, DC  20591  
  
  Phone: (202) 267-8261