For a given airspeed and model weight, the wing has to fly at a fixed Cl to generate the require lift to support the airplane. This fixes the wing AoA for that airspeed and weight. Moving the CG over the normal range does not alter the wing AoA required, except for a very small change in the stabilizer Cl.
The lowest fuselage drag will be with the fuselage aligned with the wing streamlines. This means the pod should be angled nose down several degrees with respect to the wing at it's best L/D angle of attack. The boom should also be angled down slightly. The streamlines are curved, so without making a curved boom and pod the fit is only approximate.
The up and down wash is proportional to inverse of the aspect ratio, so the higher AR ALES gliders will have less down wash than the DLG in this movie:
The Opus designed by Michael Selig is the most obvious example of this type of design (claimed 30% fuse drag reduction over a straight pod and boom,), but the Icon appears to follows this idea as well.
XFLR5 will plot streamlines that show the wake curvature, but I'm not sure how accurate they are. They show less down wash than the NACA reports indicate, and that in air testing seems to show.
The down wash angle at the tail is usually taken to be the down wash angle at infinity, which is:
Down wash angle, degrees = 114.6*Cl / (pi*AR)
Putting the boom at this angle when the wing is at best L/D AoA is a step in the right direction. Of course the whole airplane is descending downward at the glide slope angle, but that can be ignored when setting the angles since the wing's AoA at best L/D is set including this angle already.