I was having trouble visualizing the A3D wing flap to pylon interface from available pictures so I stopped off at the excellent New England Air Museum at Bradley Field north of Hartford, Connecticut and took a close look at their A3D.
In summary, the aft part of the pylon fairing is attached to the flap and pivots with it when the flap is lowered.
What I indicate to be a rub area might just be dirt and there may not actually be a pivot point between the fairing on the flap and the pylon although it seems likely that there is since there is an access panel there...
This is a Bill Spidle picture of the extended flap, showing how the top and bottom of the forward edge of the fairing on the flap have moved with respect to each other (top going aft and bottom going forward).
The inboard side of the fairing is quite different.
In another Spidle photograph, the flat area at the top of the interface is apparent.
And the view from the bottom shows that the split line between the pylon and the flap fairing is perpendicular to the flap hinge line. (This picture is actually the left side flopped but the fairings are mirror imaged.)
Why such a convoluted arrangement? My guess is that it had
something to do with the aeroelastic problem that Douglas had with the
relatively thin, high aspect ratio wing. If you can get a good look at
the pylon, you'll see that it is cambered at its aft end so as to
generate lift outboard and below the wing for some important reason,
since lift results in drag. (The purpose might be to stiffen the
pylon/engine nacelle combination by loading it to one side; it is
therefore less likely to "wobble" in roll or yaw.) The pylon is also
fairly wide at the aft end of the wing torque box, probably to provide
adequate torsional stiffness to the wing. A fairing on the pylon aft of
the wing torque box is therefore desirable to reduce drag. If you want
as much flap as possible (i.e. not have an inboard section and an
outboard section with a gap in between for the pylon fairing), then the
fairing has to be attached to the flap and if it's attached to the flap,
when it pivots it moves perpendicular to the flap hinge line, not in
parallel with the pylon, which means it can't retract within the pylon.
And so you wind up with something as convoluted as my hypothesis...
I don't know if the Trumpeter kit reflects this area accurately or not.