Transparency on the viewer display frame was always supported but the text and icons default to white. As of v3.6.5 they will appear as black when the frame color is set to None.
To make the viewer display transparent, go to in5 > Export HTML5 with in5 and in the Viewer Display section, set Frame Color to None. It sounds like you might have gotten that far but then the icon didn't show up because the icon was white and was being displayed on a white background. To change the icon to black, add the following CSS in the Resources section:
If you want the icon to be the purple color of your text, you could replace the fill with the hex number of the purple (#474077).
Pinning an object is a frequently requested feature. It's not currently available, but it might be available in a future release.
And can you describe the issue that you're having with the pdf download?