Preheat oven to 400° Fahrenheit. Place chicken breasts side-by-side in baking dish, top-side down, making sure chicken doesn't overlap if possible.
Use basting brush to brush tops of chicken breasts with melted ghee. Lightly season tops of chicken with salt, then generously coat chicken breasts with half (⅛ cup) Everything But the Bagel seasoning.
Flip chicken breasts over and repeat process with melted ghee, salt, and Everything But the Bagel seasoning on other side.
Place baking dish in preheated oven. Bake chicken breasts 25 minutes, then begin checking doneness with internal meat thermometer, adding time as needed until thermometer reads 160° Fahrenheit. See Notes for cook time estimates.
Toward end of bake time, place 1 tablespoon ghee in medium microwave-safe bowl. Microwave ghee in 15 second increments, stirring well between each, until ghee is melted but not boiling or bubbling.
Add Everything But the Bagel seasoning, softened "cream cheese", green onions, and almond milk to boil with melted ghee. Whisk well until ingredients are fully incorporated and thick "cream" sauce forms. Taste and add salt as needed to achieve desired flavor. Set sauce aside.
Once chicken reaches 160°F internally, carefully remove baking dish from oven. Set dish aside and let chicken rest 5 minutes. After 5 minutes, divide chicken into desired portion sizes, top with plenty of scallion "cream cheese" sauce, and serve warm with desired sides.