This will be not corrected on the 0.17 but I already looked into it (on the mozillazine site).
The reason there wasn't transparency. CTS does leave transparency on changed images untouched (as far as I see from the code).
But color edits can change the order in which rules are applied to elements. This is because I have to use the !important keyword to override existing definitions.
The problem on the mozillazine was/is that my bitmaps color edits overrode rules with "bitmap: none" which normally had a higher "specificity".
I will try to incorporate a workaround in a newer version. As I see no way currently to avoid the "!important" keyword (it is easier to avoid when manually creating CSS but difficult on an automated process like this) I will probably also add the unchanged bitmap:none statements with "!important" to restore the correct order. Maybe even (optional) for unchanged foreground/background color definitions.