The auto Builder still is broken in patch 1.3. The all distributed ship designs do NOT distribute defenses evenly, they focus on 1 thing. If you research shields it will place all shields on ship, if armor etc. Before it distributed defenses evenly (patch 1.1 i think), but with new patches its broken and even its logic needs update as currently the ships its building on auto are really bad- why put another beam if you can add a module and get 2x firepower?
It looks like auto builder does not know it can add higher tier modules etc. Its stuck with basic "crap".