The process involved exploiting identifiable world features such as the position of clouds, orientations of certain block textures, and more, to discover the exact coordinates of the blocks in the image (insane in itself); figuring out the exact camera perspective via regression fitting; creating and training a machine learning model to upscale the image in order to better discern details and manually create a reconstruction; deducing how the image was taken (print screen -> cropped to 512x512 -> 4x downscaled with specific resizing algorithm); and more. Through these efforts, they had significantly reduced the number of candidate seeds; distributed computing power provided by 3,500 project volunteers' GPUs was then used to obtain the final 700,000 candidate seeds, and from that a brute-force approach was used to isolate the actual pack.png seed.
The YouTuber SalC1 produced an excellent video on the project [1].