Seems like -compose copy_opacity has not been working properly for a while. It even goes back at least as far as ImageMagick-6.7.4-10. It looks like it is putting the alpha channel back, but then making the opaque parts partially transparent.
convert \( logo: -transparent white -write logo_tmp1.png \) \
\( -clone 0 -alpha off -write logo_tmp2.png \) \
\( -clone 0 -alpha extract -write logo_tmp3.png \) \
-alpha off -compose copy_opacity -composite logot1.png
