Because the PostScript imaging model does not support transparency, transparent objects must be converted by the PDF converter into opaque objects. This can result in visible colour differences because of differences in colour management between the PDF converter and the PS3 interpreter.
Images or smooth shades are always flattened into 600 dpi images.
The PDF converter does not have knowledge about the output colour space. The output colour space is handled by the PS3 interpreter. You cannot set the blend colour space to the output colour space. Instead, the blend colour space is set to the colour space specified for CMYK.
The PDF converter does not have access to the spot colour library. Therefore, if a spot colour is involved in transparency or overprint, the alternative colour in the PDF is used. Visible colour differences are possible with other areas where the spot colour is used.