To prepare grains: Combine farro, 2 cups water and 1/2 teaspoon salt in a medium saucepan. Bring to a boil over high heat. Reduce heat to maintain a gentle simmer, cover and cook until the farro is tender, 20 to 30 minutes. Let stand, covered, for 5 minutes.
Meanwhile, combine rice, 11/3 cups water and 1/4 teaspoon salt in another medium saucepan. Bring to a boil over high heat. Reduce heat to maintain a gentle simmer, cover and cook until the rice is tender, about 30 minutes. Let stand, covered, for 5 minutes.
Drain any remaining liquid from the farro and rice; fluff with a fork. Spread out on a large baking sheet to cool.
Meanwhile, heat 1 tablespoon oil in a large nonstick skillet over medium heat. Add onion, thyme and 1/4 teaspoon salt. Cook, stirring often, until the onion is browned in spots, 5 to 7 minutes. Reduce the heat to medium-low, cover and cook very gently, stirring occasionally, for 10 minutes more. Add port (or water), increase heat to medium-high and cook, stirring, until the liquid sizzles away, 15 to 30 seconds. Set aside to cool.
To prepare vegetables: Preheat grill to medium-high.
Whisk 1/2 cup oil, red-wine vinegar, balsamic vinegar, garlic, thyme, 1 teaspoon salt, pepper and fennel seeds in a large bowl.
Slice zucchini and eggplant lengthwise into 1/2-inch slices; cut onion into 1/2-inch-thick slices. Cut bell peppers lengthwise in quarters; remove seeds and stem. Core tomatoes and cut in half. Brush all the vegetables generously on both sides with 1/2 cup of the vinaigrette, leaving the remaining vinaigrette in the bowl.
Place about half the vegetables on the grill. Grill, turning once or twice, until softened and charred in spots, 5 to 10 minutes total. Remove to a large plate as they are done and grill the remaining vegetables.
To assemble: When cool enough to handle, peel the tomatoes and add to the bowl with the vinaigrette. Crush them with a spoon or your hand into a chunky sauce. Chop the other vegetables into bite-size pieces and add to the bowl; gently stir to combine. Add the farro, rice and onion mixture and gently stir to combine.
