No less an authority than Sir Gerald Burrard stated emphatically that if you had two sets of barrels fitted to the same action/stock they would impact at different points due to the greater barrel whip of the longer barrels.
It would seem only natural that an over under would have more barrel rigidity in the vertical plane than a SxS so would likely be less affected by "Whip".
One of course can always make up their own their mind whether to believe Wonko or Burrard, as for "ME" thick I'll stick with Burrard.