Transparency
If your pages are to be printed in the four process colours and are not intended to print with any extra colours (spot colours) you must be really careful not to inadvertently include any spot colours on your pages where transparency is used.

The flattening process handles spot colours in a special way and with overprints, and if a flattened file which includes spot colour is presented to a CMYK workflow, which will convert the flattened spot colour to CMYK it will probably not reproduce as expected.
Only incorporate spot colours in your layout if you know they will be used on the press.

Be careful when mixing overprinting and spot colours with transparency. To view the printed results of overprinting on-screen, enable Overprint Preview.