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 saucepan, heat the EVOO, 1 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 saucepan, melt the butter over medium heat. Whisk in the flour for 1 minute, then whisk in the milk and vegetable broth; 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.
Preheat a broiler. Add the cheese sauce to the pasta and toss. Spread half of the pasta in a 9-by-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 to 5 minutes. Serve with the crème fraîche, if using.