As well as the cover for the folded roof causing a problem, if you have the plastic cover over the dipstick/oil filler and close the lid with the cover open it can cause some movement. The lid on my F is slightly distorted because it had had a clamp on boot rack in the past. The distortion is more or less permanent but I have much better shut lines now resulting from adjusting the hinges. It is a case of trial & error.
Richard
1.8i Mk2 Solar Red, 16 inch square spoke wheels, MGFMania hood with zip-in glass rear window, DRLs, Kmaps ECU, Pipercross panel air filter, MGOC Supersports back box & some cockpit bling