Matt,

You have a lot of material there.  First, although it's merely a convention, the standard aeronautical definition of axes is X + forward, Y + out the right wing, and Z + down. We use the term CG, rather than center of mass, although the latter may be more pure.

When the battery is in front of the wings and its plane of longitudinal symmetry is in the XY plane of the model, the moment of battery w/r to the X axis of the model is zero.

When the battery is in front of the wings and its plane of longitudinal symmetry is in the XY plane of the model, the first moment of mass of the battery (its contribution to the CG) w/r to the XY plane of the model is zero.  The Z component of the first moment of mass is zero.  The first moment of mass is in a specific direction from the CG (or other reference), not a distance from an axis. The second moment of mass is the mass times the distance squared from an axis.  You may be confusing the two.

The moment of the battery w/r to the Y and Z axes of the model is equal the weight of the battery times the distance between the battery COM and the model COM.

The first moments of mass of the battery in each of the three directions is equal to the mass of the battery times the x, y, and z components of the distance from the airplane CG to the battery CG. The calculator below gives the x and z components.  Did you see it?

The ideal place for the battery COM is in the model COM but the model COM is usually inside the wing and close to the bellcrank so this location is not really feasible.

The ideal place for the mass of everything in the model is in the model COM but stuff (the wing, for example) needs to be in other places, so this location is not really feasible.  

The usual place for the battery is in front of the wings on the model center line (X axis) and this requires longer aft portion of the fuselage to balance the Y and Z moments of the battery. Longer fuselage = heavier fuselage.

For stunt planes it tends to work out the other way.  Various things set the tail length.  Reply 36 of http://stunthanger.com/smf/index.php/topic,20427.msg199505.html#msg199505 list some.  The propulsion system is usually positioned to balance the airplane after the tail location, hence the fuselage length, is picked.  Minimum second  moment of mass (moment of inertia) comes from locating the battery and motor together.  If you pick motor location for aerodynamic reasons, the battery still tends to be forward of the airplane CG.

This arrangement generates, however, the additional parasite moment of the battery about the X axis of the model and this moment affects the model position in the air but the model position in the air can be adjusted using the ailerons.

"Parasite moment" is not a conventional term.  You are talking about the moment of mass of the battery in the z direction from the CG, and that has been an issue with some of us over the last few years.  If the z position of the battery isn't right, it can give you fits trimming the airplane.  If you try to compensate with aileron, it will balance at some places and bite you in others.  For example, if the battery is too high and you level the wings with aileron in level flight at five feet, the airplane will roll in at you in the inside loop of the overhead eight, when line tension is lower, allowing the aileron effect to overpower the inertial effect.  See reply 28 of http://stunthanger.com/smf/index.php/topic,27559.0.html for an embarrassing vertical battery location story.  I recently needed to move the CG of the same airplane down.  I shimmed the battery and added heavier wheels, which have the added benefit of being quieter. 
 
I disagree with your conclusions.

Another interesting thing is that stuff on a stunt plane's fuselage centerline is to the left (for conventional airplanes) of the CG. I suspect that this could put the principal inertial axis askew with the airplane X axis, which may cause the best fore-aft leadout position not to be the best position aerodynamically.
 

On the "battery over the wing screws things up" point -- just move the leadout guides up and the motor down, for crying out loud!  Or set the battery down into the wing, or give the thing a bit of dihedral.  There's lots of ways to skin the cat.

Moving the leadout guides up might work.  Moving the motor down will change the flow over the wing, the direction of flow over the tail, and landing gear length.  Dihedral will cause lateral-directional perversions unless it's accompanied by a compensating fuselage mounted on the top (or bottom, for negative dihedral) of the wing.  Namely, dihedral has a dihedral effect.  Can you think of an airplane that would benefit from having the battery on the fore-aft (X-axis) CG?  Maybe a combat plane.  Certainly not any conventional stunter.