I'm still fumbling my way with kde4, but many items are changed as part of a theme.
Hmmm... me neither. I still need to locate the config files that sets all the desktop themes.
However you do not need to select a particular theme just to set transparency on your panel. Stick with whichever theme you like. The secret is "Customized".
After setting the your preferred theme, on KDE Control Center, navigate to Advanced User Settings > Desktop Theme Details. You will notice that the name of your theme is displayed. Click on the drop-down arrow and scroll to the top of the list and select Cusomized.
Next , choose the theme for your Panel Background. Oxygen Panel Background is more transparent than most of the default themes.
Click Apply. Nothing will probably happen. The next step is the really annoying thing about KDE 4.3.2. The changes should have taken effect on clicking Apply but you'd need to go to either your Folder View or Desktop view mode.
Right-click anywhere on the desktop > Desktop Settings/Folder View Settings > (Appearance for Folder View) > Desktop Theme > select Customized > click Apply and voila!