Bring a large pot of salted water to a boil. Add the pasta and cook just until al dente, according to the package directions. Drain the pasta and set aside.

In a large pot, melt the butter over medium heat. Reduce the heat to low and whisk in the flour to create a paste. Add the milk and whisk until smooth. Increase the heat to medium and continue whisking until the sauce starts to thicken, about 2 minutes. Stir in the shredded cheese and 1/2 teaspoon sea salt, and continue stirring until the cheese is melted and the sauce is smooth.

Add the pasta, stirring to combine, and cook just until the pasta is warmed through. Season to taste. Stir in the peas, if using, and serve with generous dollops of pesto, fresh basil, and pinches of red pepper flakes.