Military flags up to the Civil War were always square. The sizes could vary of course (the British used the 6 by 6 1/2 feet model, copied by us) while, as you have noted, Napoleonic Wars (and even later) French colors were much smaller. I have never seen anything that Beauregard wrote that stated categorically that these flags influenced his choice of sizes however.

With regards to the Southern Cross/ANV flags, the pattern was designed by William Porcher Miles in a rectangular style. This was due to the design being submitted as one of the choices for the Confederacy's first national flag. National flags are almost always rectangular. Hence Miles, who was well versed in heraldry and flags, made it in this shape. When it was brought out for discussion as a battle flag, the square version was selected due to the established practice of unit colors being square. Square flags were also much easier to make thanks to the right angles.

Greg Biggs