QuarkXPress 10 has new functionality, which helps you more advanced with transparency. Now the transparency can be handled even far-far better by QuarkXPress 10. The new PDF Pass-Through Transparency feature lets you avoid flattening while creating smaller, device-independent PDFs.
For more information please go to the link below:
http://www.quark.com/Products/QuarkXPress/Features/Reliable_Print_Output.aspx#5