Map Pilot does not touch the obstacle avoidance system. If it is on as set by DJI Go it will be left on. We have found that it causes more problems than it solves due to flying into the sun with dirty optics. This causes the aircraft to stop and hover mid mission. There is no way to resume a mission that has been stopped due to the obstacle avoidance system.
Being that Map Pilot does not support void areas within the survey area polygon the geofence option wouldn't work.
The ways to do this using Map Pilot would be to manually snake a linear flight path around the areas you need or do a mission with concave cutouts around the tower(s) and then do a separate mission to close of the top area. Picture a C shaped area around the tower and then and I shaped mission to close it off.