The function used is the scout function, which is the mean by default:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#Scout_function
We do not recommend using this process "Downsample to atlas", it creates files that are difficult to manipulate, and as you reported, not very intuitive. I'd recommend you use the process "Extract > Scouts time series" instead, it would give the same results, but as a "matrix" file (68 signals) instead of a "source" file (source maps displayed in 3D).