I wouldn't worry about the strings above the bridge, generally with a straight edge on the centerline of the fingerboard it should hit the top of the front of the bridge precisely. This is with string tension.
The general set up including nut, fret and saddle set up will be fine if you get this earlier measurement right.
If by U shape you mean the nut in which to adjust the rod, it lays flat on the bottom of the routing slot.
Are you having the adjustment done at the headstock?
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