Bring a large pot of water to a boil, salt it, add the pasta and cook until al dente. Drain, then return to the pot.
While the pasta is working, using a food processor, pulse the tomatillos until chopped. In a medium size saucepan, heat the EVOO, one turn of the pan, over medium-high heat. Add the onion, garlic and jalapeños and cook for 5 minutes. Stir in the tomatillos, honey and cumin; season with salt. Simmer over low heat for 10 minutes. Stir in the cilantro and lime juice.
In a medium size saucepan, melt the butter over medium heat. Whisk in the flour for 1 minute, then whisk in the milk and vegetable stock; season with salt and pepper. Bring to a simmer and cook, stirring, until thickened, about 5 minutes. Stir in the Swiss and Monterey Jack cheeses.
Pre-heat the broiler.
Add the cheese sauce to the pasta and toss. Spread half of the pasta in a 9-inch x 13-inch baking dish and top with half of the tomatillo sauce; repeat the layers. Sprinkle the chips and pepper Jack cheese on top. Broil until browned, 3-5 minutes. Serve with the crème fraîche, if using.