There used to be transparent explorer backgrounds in Windowblinds but that's not supported anymore.
You can use a utility like WindowsFX which is part of Object Desktop or you can do it with Windowblinds Alpha adjustment in Skin Studio. The easiest way is download one of my skins, Alien Technology, it has a plugin that lets you set the individual window's transparency.
Be aware that transparency can slow your machine down if overused.
doh! just read your original post all the way through and I see you already know about WindowsFX and WB...
I doubt that the inactive state has a transparency setting, it's probably a coincidence that it looks like it's under the focus window.
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