The support matrix is right: Java GUI testing is not supported by Coded UI Test.
Generated code from recoded MTM test-case uses native windowsWindows OS
elements to work with and all actions (mouse clicks & key typing) are linked to them, e.g.:
...
Mouse.Click(someClient, new Point(239, 90));
Mouse.Click(someClient, new Point(139, 193));
Mouse.Click(someTitleBar, MouseButtons.Right, ModifierKeys.None, new Point(233, 9));
...
MTM can record actions on Java GUI just because it uses Mouse.Click(obj, point)
and key typing events, the first one uses coordinates from GUI elements that treated like Windows native (window & it's titlebar)