I supect when both companies started offering digital services in 2000 or so, they signed a corporate-wide deal with Motorola for their headend equipment and boxes. Atlanta and all other systems for both companies would have fallen under such an agreement.
Comcast and Charter have since acquired several systems since that time that utilize Scientific Atlanta equipment. It would have been a major cost and logistical burden to change over to Motorola equipment, so the SA equipment they inherited remains in use. This is true with the former Adelphia systems Comcast acquired in Cartersville, Canton, and Cumming.
After having service with both boxes (SA under the defunct Acworth Cablenet, and Motorola under Comcast), I think the Motorola boxes are 1000x better. I had frequent issues with the SA boxes, and their automatic 1:15 AM shut off (power saver feature) is really annoying for someone who keeps their TV on at that time. Motorola boxes run much faster and don't shut off automatically (instead...they like to stay on, especially if you have a DVR).
Also...SA is now a division of Silicon Valley based Cisco Systems (although the SA division HQ remains in Lawrenceville).