Acrobat 5 (PDF 1.4) and above supports supports transparency, so it isn't flattened. If the RIP can't reliably flatten transparency, stick with Acrobat 4 (PDF 1.3). Out of interest, what is the RIP, and which version?
Harlequin Rip version 9 rev2. I did find that in indesign under edit menu there is a Transparency flattening preset menu that lets me use the newer version of PDF output's.
The Transparency Flattener Preset menu lets you define Transparency Flattener Preset, but they aren't actually used unless your printing direct from InDesign or exporting to a PDF version that doesn't support transparency.
What are you trying to accomplish? To create PDFs over version 1.3, but that have flattened transparency? I can't imagine a purpose for such files. We have a Harlequin RIP a version older than yours, and as a rule I feed it PDF/X-4 files (PDF 1.6). The only problem I've seen is transparency on spot jobs generating empty CMYK seps.