First of all, trees don't "heal" in the sense that wounds on people heal. Our bodies regenerate tissues in much the same form of the tissues that were removed (to a limited extent). Trees compartmentalize wounds, generating woundwood over the wounded area. Flush cutting removes the "branch collar," creating a larger wound than if the branch were removed outside the collar. Also, it is likely that some of the parent branch tissue will be removed. The spread of decay inside the tree is greater with flush cuts.