Melt butter in large skillet over medium; cook onions 15-20 minutes, stirring occasionally, until golden and caramelized. Add balsamic in final minute; cool slightly.
Mix cream cheese, sour cream, and mayonnaise smooth in large bowl.
Add 1½ cups Gruyere, mozzarella, garlic powder, thyme, salt, and pepper.
Fold in onions and three-quarters of bacon; reserve remainder for topping.
Transfer to slow cooker; smooth top and add remaining ½ cup Gruyere.
Cover; cook on low 2 hours or until hot with bubbling edges.
Top with reserved bacon and chives; serve warm with crackers, bread cubes, or vegetable sticks.