Panel window can be semi-transparent when they are floating. This makes the panel windows a little like a HUD (Head Up Display) in a game.
Panel transparency is only available if the panel is floating and the "Enable transparent panels" option is enabled inside the Options > Preferences: Display. See: Display Options.
When a panel window is transparent, you can click through it to the text below it, as long as you are not clicking inside an object within the floating window.
To adjust the transparency amount, click on the transparency button in the panel’s window-control toolbar.