Mikael
Are you pondering a flag for your own respective display use, or are you looking to make something authentic for field use?.
Volumes of books and many decades of research has been put into the vexillology examination of Confederate flags. As with many other war related items, the flags also evolved and changed over the course of the war. Many were specific to theater, date, and commands, especially true in the AOT. No not all AOT battle flags were rectangular. Different makers and depots had their own patterns and resulting design characteristics. Many times we can determine when, where and what depot may have made a particular flag by these small characteristic details.... Again depends on who, and time and place. Unfortunately its difficult to correctly have one particular generic flag that will or could properly fit into any and all given scenarios and time frames. Regardless what we commonly see some reenactment units using....
Most Regiments went through on average around 2-5 flags over the course of the war... worn out, damaged, lost, captured, etc. Each new issue might have been very different than the previous... What a regiment carried at Shiloh, may be very different what the same regiment had in their hands at Atlanta.... Did you have particular unit or targeted time/place in mind?...
On another related note... Many of these flags were assembled using specific (then) known sewing formats and methods that to most modern sewers is a near complete foreign and obsolete concept... Many tend to apply modern methods, and the result rarely looks like or matches the original product. Most times one needs to have and possess a really really good level of knowledge and skill of period sewing methods before trying to take on this type of challenge... Yes anyone can grab an electric Singer and slap something together that to them might "look close"... but to others might not be as much... The pattern, details and assembly methods is what typically determines a good looking reproduction flag from a really farby one... A Battle flag produced through Richmond has its own unique pattern characteristic that differs from others made through Charleston, Atlanta, etc... Materials... this is another acute limitation factor upon making an authentic flag. Originals beyond 1861 were normally produced using worsen wool bunting.... Unfortunately no one makes this material anymore as it was replaced on the flag making market with nylon back in the 1940-50 era. Close as can be had is alternate fabrics labeled as "wool blend", cotton blend, or other blends of natural/synthetic fibers that try somewhat to replicate the loose weave bunting...