Personally, I like the fact that the script maker window is always on top.
Due to the fact that the Script Maker Window is no longer "Confined" within the window of the application, it does not surprise me at all that Ctrl-Tab no longer works. Ctrl-Tab is a shorcut to cycle through the open Windows. Since Script Maker is no longer a "Window" but rather Modal, I think this is acting how it should.
I think this is expected behavior now that script windows can live outside the application window in 11. They no longer display on the Windows menu and they are always on top. Between this "feature" and the multiple Inspector windows (all without keyboard shortcuts, by the way), it seems we now need to get a third monitor for development.
Well good thing I have 4 then. ;)