Stir together the tomato, scallions, jalapeño and salt in a small bowl. Set aside.
Toss together the cheeses and flour in a bowl. Set aside.
Heat the olive oil in a heavy saucepan over medium-high heat. Add the sausage and cook, stirring occasionally, until browned, about 5 minutes. Use a slotted spoon to transfer the sausage to a bowl.
Add the onions to the saucepan, reduce the heat to medium-low, and cook, stirring occasionally, until softened, about 5 minutes.
Add the beer and cook, scraping up the browned bits from the bottom of the pan, about 1 minute.
Start adding the cheeses, a handful at a time, stirring until melted. Continue adding the cheese in this manner, stirring constantly, until all the mixture is melted and smooth. Stir the sausage into the cheese mixture.
Transfer the queso fundido to a warm serving bowl. Spoon the salsa over the queso, using a slotted spoon to drain the excess liquid. Serve at once with tortilla chips.