I am not an expert, but as far as I know the solution would be to place exclusion zones on the sceneries you generate. It would be multiple exclusions zones, objects, facades, forests, roads. I think that can be achieved in Overlay Editor or in WED. Placing your airports higher in the sceneries hierarchy in the scenery_packs.ini would ensure that the airport show all their glory. This would limit the exclusions of auto-generated objects to only your photo-sceneries.
I hope this can be a lead for more informations on the websites of Laminar, WED or Marginal …