Can I make the pinboard transparent, like in the 1.2.x series?

No. Please don't ask about this. The old method doesn't work properly with Gtk+-2.0, is slow, ugly, and doesn't follow the WM standard. KDE, GNOME, XFCE and ROX all use a single screen-sized window for the backdrop now.

ROX provides plenty of support for setting the backdrop itself and allows external programs to choose a backdrop. See the Wallpaper application for an example; this program chooses a random backdrop
each time you log in, and can also be used to put the output of other programs, such as XEarth, on the backdrop at regular intervals.

Root-portal can be used to show log messages on the backdrop, replacing the old roottail. Deskmenu can be used to provide a custom root menu.

See this discussion for more details.