Cut solid sections of squashes into large chunks and seed-pod sections into 3/4-inch-thick wedges. Puree onion, garlic, and 1 tablespoon water in a blender until smooth.
Heat oil in a 4-quart pot over medium heat. Add mustard seeds, fennel seeds, and coriander, and cook until fragrant, 1 to 2 minutes. Stir in onion paste and ginger. Cook, stirring often, until caramelized, 6 to 8 minutes.
Add tomato paste, scraping bottom of pot if needed. Stir in remaining 3 cups water, the salt, and crushed red-pepper flakes. Add squash, and cover partially. Bring to a boil. Reduce heat, and simmer gently until squash is tender, 12 to 15 minutes. Serve over brown rice with cilantro and lime wedges.