The "single atlas" for data export means one atlas for multiple skeletons. The atlas may still have multiple pages if the images don't fit on one page. Each PNG that goes with the atlas data file is a "page".
There is no setting for reducing the scale until the images can be packed into a single atlas page. Most games would not want their export quality sacrificed like that. You'd need to pack multiple times, reducing the scale each time, until you find the largest scale that packs into a single page.
If you are packing a PNG export, the atlas having multiple pages usually makes little difference compared to fitting it in a single page. Mainly it takes up more memory but there isn't an issue with draw calls that rendering skeleton data can have when there are multiple pages.