I keep my trees on the ground mulched in, but more than anything I keep them protected from the wind. Wind chill definitely can effect your trees the same as it does us. Wind chill can significantly increase the risk of frostbite on us, even at relatively mild temperatures if the wind is strong enough, same goes for any other living organism. This is why cold frames etc are good, the temperatures are generally similar to outside, but it gives trees the needed protection from the wind. You don't want them closed up too tight or daylight sun may cause your poly tunnel to warm up like a greenhouse and risk breaking dormancy, all you really want is for it to be a wind break. Mulched into the ground, the ground will keep the roots warmer than the ambient temperature and work as a heat sink. Unless you have trees not suited to your USDA zone then they should be just fine. One of the biggest reasons native species are some of my favorites is I never have to really worry unless it's a long period of sub zero temps, they are already suited to the climate here.