This is still an issue on 5.5.4, all the paths in the “Default Uncontrolled Changelist” are in the engine itself (C:\Program Files\... rather than the project). P4V does not show any of these files.
If you do Revert uncontrolled files it starts to delete some files too (I had 8801 uncontrolled files, 909 were deleted).
If you then try to close the editor (after the revert), and open it again, the editor will crash. You need to verify the editor again for it to work. Then you get Assets to check for reconcile: 8,814) again.