Dear Andy,

Thank you for the very clear question! QuickNII exports only the slices from the atlas. This way the actual files are going to be small, and users can create their mixed images (section+overlay) using the software of their choice, typically using higher resolutions than what QuickNII supports. The downside is that users have to it.

If you have a preferred software package to handle images, the steps would vaguely be
1) open the secion image (s49_s6_20x_tile_Z_7x7.png)
2) add the segmentation as a secondary layer (s49_s6_20x_tile_Z_7x7_maxprojection-Rainbow_2017.png)
3) set the size of the secondary layer to be the same as the section image, disregarding aspect ratio
4) set transparency or any other blending method to create the mixed image.

If there are no contenders, a more-or-less suitable free software is Paint.NET (https://www.getpaint.net/), there these steps look like this:
1) open the secion image (s49_s6_20x_tile_Z_7x7.png), using "File"/"Open..."
2) add the segmentation layer (s49_s6_20x_tile_Z_7x7_maxprojection-Rainbow_2017.png), using "Layers"/"Import From File..."
3) stretch the segmentation via dragging the circle in its bottom right corner, drag it to the bottom right corner of the entire image
4) change "Quality: Bilinear" to "Quality: Nearest Neighbor" to remove blur
5) set opacity and optionally adjust the blending mode too, using "Layers"/"Layer Properties... (F4)"

I hope this helps.
Best regards,
Gergely