Power-of-two atlases
Older graphics hardware, and some mobile WebGL contexts, still prefer textures whose sides are a power of two. Sheetpack rounds the packed size up to the next power of two, and caps the free atlas at 1024×1024. If your frames would overflow that cap, shrink them first or wait for the Pro 4096 cap.
Empty padding at the bottom or the right of a power-of-two atlas is normal. It is cheaper, on most GPUs, than a tight but odd-sized texture. The JSON and CSS only address the pixels that actually hold a frame.