Is there a reason or is it just a coincidence?
The difference between Southern and Northern flags is not just coincidence. Southern flags tend to be inspired by Confederate symbolism. So Georgia's flag is based on the Stars and Bars flag, Arkansas's is based on the Battle Flag, Mississippi's incorporates the Battle Flag directly, North Carolina's is based on the flag raised by secessionists in 1861, etc. On the other hand, Northern "seal-on-a-bedsheet" flags look a lot like Union regimental flags.
You might like to try asking this question over at /r/vexillology