Right, that I get, but even for weapons that are mounted on the top, some of my effects seem to appear drawn under the ship.
Example: the energy hardpoint on the Shuttle is coords -0.227;0.000;-0.203, so from the cockpit it's toward the back and elevated slightly. Should be well above the centerline of the ship (since it's a roof-mounted turret). But if I fire a non-beam projectile from it, the projectile isn't visible until it move out from the location occupied by the ship; for all intents and purposes the shot appears to be either inside or under the ship, instead of originating above it.
Not a huge priority for you guys, it just looks a little jarring to me now that I've noticed it. For smaller, darker shots it barely even registers but you can see the effect clearly if you use a slow-moving missile projectile or a brighter sprite.