Yes, those simply are the official colors from Allen. Like here: http://atlas.brain-map.org/atlas?atlas=1&plate=100960264#atlas=1&plate=100960264&resolution=11.97&x=5400.032784598215&y=3807.9077849217824&zoom=-3 - colors are just reused countless times.
However it may be worth pointing out here that the two kinds of PNG sets are more meant for a quick view than for further processing. For the latter purpose the ".flat" files may still be a better choice even with their weirdness, https://www.nitrc.org/plugins/mwiki/index.php?title=visualign:Flat_file_format

But, the request is doable too, it's already there: VisuAlign has its atlas data in its "cutlas" folders, ABA_Mouse_CCFv3_2017_25um.cutlas may be the one in use here. Inside the folder there is a NIfTI file with the actual segmentation and a text file with the label descriptors (there is a short summary about the structure at the beginning of the file). Technically it's an ITK label file, just there are some labels with extreme high values, which ITK Snap usually refuses to load (but I haven't tried recently).

I hope this helps, best regards,
Gergely Csucs