Start by preheating your oven to 400°F and lining a baking sheet with parchment paper. While the oven heats, gently rinse your squash blossoms and lay them on a clean towel to dry completely. Moisture left on the petals can make them soggy once baked.
In a bowl, combine the ricotta, Parmesan, egg yolk, garlic, basil, chives, lemon zest, salt, and pepper. Stir until everything is fully incorporated but still slightly textured. You want the filling thick enough to hold its shape once piped inside the blossoms.
Gently open each blossom and remove the inner stamen, being careful not to tear the petals. Transfer your filling to a piping bag and pipe about a tablespoon into each blossom, then gently twist the top closed. Treat them delicately, since a little rustic shape is part of their charm.
Arrange the stuffed blossoms on your prepared baking sheet and lightly mist them with olive oil spray. Bake for 12 to 15 minutes, until the petals look tender and slightly golden at the edges. If you want a bit more color, broil for the final minute while watching closely.
While the blossoms bake, warm your marinara sauce on the stove. Spread it across a serving plate, then arrange the baked blossoms right on top. Finish with an extra pinch of flaky salt, a little more lemon zest, and any of your favorite toppings.