Here is a curious observation. Using transparencies fixes one image where PDF Tools (and some web-sites I tested) show an image part that is not visible in the original PDF and not in the version with transparencies. Acrobat extracted this correctly using white instead of transparencies, but the black Tools (and web-sites) versions adds the extra bit.
No idea how this happens, because this definitively is no transparent or even solid color part. Maybe there is some alpha-channel information in only those parts? Look at the bottom part of this image (reddish extra frame).
Anyways, the transparent version corresponds to the PDF version, so it's good to have transparencies as an additional option now.