Make the chili: In a slow cooker, combine the ground beef, onion, diced tomatoes, kidney beans, black beans, chili powder, cumin, and salt. Cover and cook on low, stirring often, for about 6 hours, or until the onions are tender.
While the chili cooks, make the quick pickled jalapeños: In a small saucepan, combine the vinegar, water, salt, sugar, garlic, and lime zest. Bring the mixture to a boil over medium-high heat, then reduce the heat to low and simmer until the salt and sugar have dissolved, about 2 minutes.
Add the jalapeños to a medium heatproof bowl or large mason jar. Carefully pour the pickling liquid over the jalapeños, making sure they are fully submerged. Let the pickles cool to room temperature, about 1 hour. Cover the bowl with plastic wrap or seal the jar and transfer to the refrigerator until ready to use. The pickled jalapeños will keep in the refrigerator for up to 2 weeks.
Make the chili cheese fries: Preheat the oven according to the French fry package instructions.
Spread the French fries in an even layer on a rimmed baking sheet. Bake for 3 minutes less than the package instructs.
Remove the fries from the oven and top with several large scoops of chili. Sprinkle the shredded cheese evenly over the top. Return to the oven for about 5 minutes, or until the cheese has melted completely.
Dollop the sour cream on top of the chili cheese fries, then garnish with the scallions and pickled jalapeños. Let cool slightly, then serve directly off of the pan.