Hi Wade,
When the Process Console window (or any explorer window) is docked, it is a child of PixInsight's workspace, just above image windows. Since process windows are top-level windows, they are always above the workspace and all of its children, on top of the main application window. This is the natural Z order, imposed by the hierarchical structure of the application's graphical interface, which follows the general design of an MDI (multiple document interface) application.
The only way to get what you want is making every window a top-level window, including tools, images, explorers, dialogs and control windows. That would break all existing logical relationships between the different elements of the GUI.
You can try undocking the Process Console window (by selecting the Floating placement option). This will make it a top-level window, which can be brought to the top of the Z order stack by just clicking on it.