In a pot over medium- high heat, add the water and nondairy milk and bring to a low simmer, 5 to 6 minutes, whisking occasionally to prevent burning. The mixture will get foamy.
Turn the heat down slightly to keep the liquid at a low simmer. Whisk in the nutritional yeast, apple cider vinegar, tomato paste, Dijon, sea salt, and cayenne, until well combined. Add the macaroni and stir. Cook the mixture over a low simmer, uncovered, for 7 to 8 minutes, until al dente. (Double- check your pasta’s package directions because the cook time will vary depending on the brand and what the pasta is made from.) Stir the mixture constantly to prevent sticking.
When the pasta is done, the sauce will look a little thin. Take the pot off the heat and stir in the vegan cheddar shreds, vegan butter, and black pepper. Cover the pot for 1 to 2 minutes and then stir with a wooden spoon until the sauce thickens up and the cheese is completely melted.
Serve with extra ground black pepper, if desired, or level up your mac 'n’ cheese with one of the variations that follow. To reheat leftovers, add 1 to 2 tablespoons of nondairy milk and heat over medium-low until warmed through.