I would not try fitting it in the trunk. Go outside with a measuring tape, measure the stock hood, then try with the tape measure set at the hood's measurement, to fit that into the trunk. The stock hood is ~56 inches wide, even if you try to turn it at an angle it's not going to give you enough room to allow it to fit in there easily. Very good chance of damaging the hood since size matters, and padding would add to the size.
When I had to pick up my XC hood (it was padded), I strapped it down on top of my other hood with soft, flexible bungie cords. It looked raised up, but didn't move at all.