While water heats, in a wide skillet, melt butter over medium heat.
Once melted, stir in flour until a paste is formed, and cook 1 to 2 minutes until paste is a light blond color.
Stir in milk and add nutmeg. Bring to a gentle simmer until milk is thick enough to coat the back of a spoon.
Stir in dairy-free cheeses, and continue stirring until sauce is smooth and gooey, then turn heat off.
In a small skillet, heat olive oil to medium, and stir in panko, parsley, and granulated garlic. Cook over medium heat 2 to 3 minutes, until breadcrumbs are browned. Remove from skillet, and set aside.
Gently drop gnocchi into boiling water. After 1 minute, add broccoli to pot, and give it a stir. Cook an additional 2 to 3 minutes, until gnocchi floats to the top, then strain.
Fold gnocchi and broccoli into sauce, and return to medium heat, if needed to heat through.
Transfer to a serving bowl, and top with bread crumbs, and a pinch of chili flakes. Serve immediately.