Combine the milk and rice in a medium saucepan over medium-high heat. Scrape the vanilla bean seeds into the milk and add the whole bean. Bring the mixture to a boil, then reduce the heat to medium-low and simmer for 25 to 30 minutes, stirring often, until the rice is tender and the mixture is creamy. Stir in ½ cup of sugar, the lemon zest, vanilla extract, and salt and discard the vanilla bean. Cover with plastic wrap and chill in the refrigerator for about 4 hours, until cold.
Preheat the oven to 375°F. Toss the strawberries and blueberries with the remaining ¼ cup of sugar and arrange on a small rimmed baking sheet. Roast for 10 to 15 minutes, until the berries are soft and tender. To serve, transfer the rice pudding to bowls and spoon the roasted berries over the top.