If you're buying or leasing the car, you can have a small receiver added that will let you insert a wheelchair carrying device. That way you preserve the trunk space and have much less risk of scratching things.
If it's a rental or being borrowed, then the trunk is your option. However, you have another way of getting it into the trunk. Drop both rear seat backs and put it into the trunk through that opening, then put the seats back up. That'll make a larger opening that could be less of a fight than doing it from the rear of the car.
If it's a rental or being borrowed, then the trunk is your option. However, you have another way of getting it into the trunk. Drop both rear seat backs and put it into the trunk through that opening, then put the seats back up. That'll make a larger opening that could be less of a fight than doing it from the rear of the car.