Mix Greek yogurt, lime zest, lime juice, cilantro, and vinegar in a medium bowl; season with salt. Cover and chill at least 1 hour or up to a day.
Filling and Assembly
Preheat oven to 400° F
Heat 1 Tbsp oil in a large skillet over medium-high heat. Cook beef, breaking up with a spoon until cooked through, about 5 minutes. Transfer to a large bowl.
Reduce heat to medium. Heat remaining oil in a skillet.
Add onion and garlic; cook, stirring occasionally, until just beginning to brown (~ 5 minutes)
Add tomatoes to skillet; cook, breaking up, until thickened, 8-10 minutes.
Add beef, chili and Worcestershire sauces, garlic and onion powders, coconut sugar, and cumin. Cook, stirring, until flavors meld, 10-12 minutes.
Spread in a 9 x 13" baking dish; bake until crust forms (~ 30-40 minutes)
Serve the filling in shells with toppings.