The new soft masking or drop-shadow transparency features automatically begin flattening after the PostScript is normalized to PDF. Similar to handling transparency-rich documents from InDesign or Illustrator software, there are some techniques that can help you avoid surprises.
First, keep black text on top of all other objects during layout. The flattener preserves your text as vector objects as long as it is not "under" any other objects. Remember that the flattener looks at the outer extent of the bounding box of your text, not just the text itself. Make sure the entire text box is on top, even corners.
Second, create spot colors in their "final" condition before writing Postscript files. The flattener treats objects differently if they are spot colors versus process colors. If you really want objects to appear only as CMYK, adjust the color definition in the layout software rather than waiting until refine processing. If spot color conversion is unavoidable, it is recommended that you enable the Overprint Handling (CPU Intensive) option in the Color Match Overprinting Objects area of the Match Colors section of the refine to PDF process template. In addition, ensure that the Set Colors to Knockout check box in the Overprint Conversion section is disabled.