I thought that the Confederate Battle Flag was always square except for its use as a naval ensign, and until later when it was used in the form of a canton on a white field with a red bar on the fly end (Stainless Banner).
The rectangular flag was also the “Official” Naval Ensign. The White Flag with the canton in the upper left hand corner with the red bar on the fly end was the official “Government” flag. It replaced the “Stars and Bars” which was confused with the U.S. Flag on the Battlefield.
Actually, the red bar was added to the “Stainless Banner” only a few months before the War’s end because the flag was confusing as well, being sometimes confused with a white flag of surrender.