Bring a large pot of salted water to a boil over medium-high heat. Cook the pasta until just al dente, about 6 to 8 minutes, then drain and set aside.
Heat oven to 400ºF (200ºC).
Heat a medium saucepan over medium heat, add the butter and allow it to melt. Add the shallot and sauté, stirring occasionally, until soft and translucent, about 6 minutes. Add the truffle oil and heat through. Whisk in the flour and let cook, continuing to whisk frequently until the mixture is golden brown, about a minute.
Add the milk, whisking to combine. Cook, stirring occasionally until the mixture has thickened, about 5 minutes. Slowly whisk in 1½ cups of the cheddar cheese until completely combined. Add the lobster meat, 1 tablespoon of the chives and the pasta, stirring to combine.
Spread the mac and cheese mixture in a baking dish and top with the remaining cheddar and Parmesan cheese. Bake until the top is golden brown and bubbling, about 20 minutes.
Top with the shaved truffles and remaining chives then divide among warmed pasta bowls and serve immediately.