Paths in the air can be removed if you deactivate the taxi blue signs; not sure how they are related but so it is. Maybe the hold short boxes can be deactivated too, but I don’t know how to do it yet.
It is possible to create your own flight plan in a mission, or at least I am doing so in cargo missions. Just select the mission and create a flight plan with the EFB before starting the flight, then load it to avionics when the aircraft is ready to taxi.