This is a historic fudge - in part because the signage is a bit inconsistent, in part because what I have done is the sort of thing that wouldn't have been allowed in the CHM days.
I've made the lower deck a loop of the A2, linking to the A2 at both ends. The A5 will be truncated to the upper deck junction, the A40 will continue to reach the main A2 at Foyleside Roundabout.