Holes are caused by woodpeckers that are after the worms. The roots of big trees are coming up above the grass. This is normal for some varieties of trees and root removal could damage the tree. Over a period of time minor roots could be removed a few at a time but not major ones. It is not recommended.
Seeds are bright red, beanlike, and are extremely poisonous.
Check in 24 hours for germination. No, unless to raise the level of bottom branches or to remove rubbing branches. Avoid watering tree trunk which could cause rot. Leaves of magnolia tree are mottled, turning brown and dropping. Magnolias naturally shed last years leaves and replace with new leaves.