I can't answer your question about freeboard having never seen the WD double, however, with likely over 400 hundred pounds of people, kayak, & gear a couple of pounds of extra epoxy won't make a diifference to the waterline.  Compare your photo with the photo here  http://www.clcboats.com/shop/boats/kayak-kits/recreational-kayaks/wood-duck-double.html with a smaller kid in front.  Being low to the water will make it easier to paddel, esp if there is wind.

You seem to be sitting high in the kayak, do you have a thick seat?

Ralph

I wouldn't be concerned with the fore/aft trim you are experiencing.  I just launched a new wood duck double two weeks ago and the freeboard around the aft part of the cockpit is pretty low, but isn't much of an issue either.
In my case, the typical loading is me in the aft seat and one or two young children in the front seat, so I have set up some special seat positions.  When using the boat with the kids up front, I move my seat forwards forwards until I run out of footbrace.  This limits the bow up trim so that the boat does not slap when going through waves.  I planned the aft footbrace locations to be forward to allow for this arrangement.  The seats are secured with velcro and the back band positions utilize plastic clips to allow for multiple options.

So far I haven't paddled in any rough conditions yet, but I have paddled with different sized people in front.  For sure, it is a different boat with a regular adult in the forward seat, instead of the usual single 5-year old.  I did decide to have a rudder and this seems to help me keep the boat on track, so I might not be noticing any funky tracking behavior.

You might want to experiment with moving one or both seats slightly forward when you have someone small in front if you feel like th bow is pointing up in the air.  This probably won't change the amount of aft freeboard though.

I am planning to post pictures as soon as I can gather the photos from everyone elses phones and cameras!