Browsers handle Live 3D files better than Adobe Reader does.
Adobe's handling of 3D, and transparency in particular, is quite limited. Adobe Reader does not correctly sort translucent triangles back-to-front when rendering. This is a known problem in Reader since version 7.0, which Adobe has not fixed.
So, you will not be able to produce a PDF with transparency/translucency that will look as good as it does in a browser window.
Here are a couple of things that you can try when preparing a 3D model for PDF output:
- Avoid having meshes in your model that are too close together, this can interfere with the way the way it renders, especially in a PDF.
- Try to design the model so that transparent surfaces can never overlap visually.