It sounds to me that you’re still using the unreleased and now obsolete com.unity.ui.runtime package. If that’s the case, please uninstall it and install the new com.unity.ui package. More info here:
I think the above issue was solved in the new implementation of runtime, where Panels are now assets (in the form of PanelSettings asset) and what you have in the scene are UIDocument components that can share a Panel. There’s no reason why you should need 2 panels to do a console window on top of another part of your UI. You do all this in the same panel, by just displaying a different subtree of elements on top of the existing elements. Focus would then be handled properly by default.