Hi Tim,
The square holes? Have a look at the following picture of AP2289's chassis fab. The square holes seem to line up with the horizontally/longitudinally placed square tubing (tapered toward the rear) that forms part of the cage for the diff. and also provides mounting locations for the rear suspension. Why are there holes at their junction with the rear panel in the cockpit? Maybe it's just so that it's easier to guarantee full penetration for the crucial welds.
Craig or Warren....feel free to correct me
Cheers,
Glen