Combine salt, thyme and pepper; sprinkle over roast.
Place roast in a shallow baking pan.
Bake, uncovered, at 325° for 2 to 2-1/2 hours or until a meat thermometer reads 160°. Meanwhile, in a skillet, saute onions in butter for 8-10 minutes or until tender. Stir in flour, lemon juice, bouillon, salt, nutmeg and pepper; add water. Cook over medium heat for 2 minutes, stirring constantly.
Cut roast almost all the way through into 3/8-in. slices. Spoon 1 tablespoon of stuffing between each slice. Spoon remaining stuffing over roast.
Bake, uncovered, at 325° for 30 minutes If desired, thicken pan juices to make gravy.