There is no way to save out of Pages to pdf without flattening the transparency.
Proposition: In any save path, transparency is flattened in saving.
Test of proposition: Apple Pages '08 and Apple Mac OS X 10.4.11 as platform.
1. Launch system software and application software.
2. Insert first composition frame, select Apple Hoefler antiqua at 24 US pt, enter 'Type', leave default colour, leave default opacity.
3. Insert second composition frame, select Apple Hoefler antiqua at 24 US pt, enter 'Transparency', change default colour to rubrication red, change opacity to 50%.
4. Select e.g. File > Print > PDF > Save as PDF, name file 'Test', and select folder.
5. Launch Acrobat Professional 6 (first version with ISO 15930 PDF/X-3 verification), check the PDF version (: 1.4), check at high magnification (: no rasterisation), check that the source character string can be synthesised (: it can).
As posted previously, if transparency is applied, PDF 1.4 is automatically configured unless the path is ISO 15930 PDF/X-3 that does not support transparency (PDF 1.3 has an opaque imaging model, not a transparency imaging model). This is a simplistic test, but it is nonetheless a test.
Because Apple Quartz has applied transparency since 2000, and because there the matrix of system versions and application versions is somewhat monstrous, the notion of testing is somewhat notional 🙂.
/hh