The problem is that the "Weapons" box is still sized big enough for 4 weapons, although it only displays slots (grey boxes with a keyboard shortcut number) for two of them. The "Drones" box is only big enough for 2 drones, although all 4 do appear and are selectable. The 4th one goes behind the subsystems box! So it's just a cosmetic flaw, but quite an annoying one.

(context image: http://imgur.com/a/rCZuB)
I've specified <weaponSlots>2</weaponSlots> and <droneSlots>4</droneSlots>, and made sure the raven.xml file only has two <weaponMounts>.
I'm sure it must be possible to avoid the standard 4/2 sizes, because the Engi ship has 3/3. Can anyone suggest what I'm doing wrong?