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I have observed that when Starting the application and Z order is set to Pinned to desktop, and the transparency is set.. the transparency is ignored and it is pinned to the desktop solid.
However, when changing the Z order to Regular, then closing and reopening Console and then setting the transparent console window to "Pinned to desktop" it works as expected maintaining the transparency while being pinned to desktop.
Please report this in Bug Reports tracker. It will get lost in here.