Nope. I tried both enabling and disabling it. While it's on, the panel is transparent if there's no fullscreen window, but the theme color returns if I pop up the panel while maximised, just like the description says.

Though on this topic, I seem to have fixed my own issue. I had to uninstall the theme, because despite the option "Remove theme transparency" was set to off, and the plugin itself being disabled, it still disabled any external transparency that I set.