Preheat oven to 350 degrees. In a medium bowl, whisk together flour, wheat germ, and 1/4 teaspoon salt. Set aside. In a medium skillet, heat 3 tablespoons oil over medium. Add half the chard to skillet, season with salt and pepper, and cook until chard wilts and releases liquid. Wipe skillet, set aside.
Add cooked chard to flour mixture and mix with fork to incorporate. Transfer to a 9-inch pie plate; firmly press mixture into bottom and up the side of pan. Bake until golden and firm, about 25 minutes. Cool.
In reserved skillet, heat remaining tablespoon oil over medium. Add onion and cook, stirring occasionally, until softened, 3 to 5 minutes. Add remaining chard to skillet, season with salt and pepper, and cook until wilted, 2 to 3 minutes.
Transfer chard mixture to a colander. Press firmly with the back of a spoon to squeeze out as much liquid as possible. Top prepared crust with chard mixture and cheese; place on rimmed baking sheet.
In a medium bowl, whisk together eggs, milk, nutmeg, mustard powder, 1/2 teaspoon salt, and 1/8 teaspoon pepper. Pour custard over chard mixture. Bake until custard is set, 40 to 45 minutes. Let stand 15 minutes before serving.
Serve this quiche either warm or at room temperature.