Remove chuck roast from the refrigerator and sprinkle with salt all over. Leave at room temperature for 45 minutes.
Preheat the oven to 325 degrees.
Mix together 2 tbsp of olive oil, black pepper, garlic powder, smoked paprika, thyme, and crushed red pepper flakes, and brush the mixture onto the chuck roast.
Preheat a cast-iron skillet to medium-high with the remaining olive oil. Sear the roast on all sides; this should take about 8-10 minutes. Transfer the roast to a roasting pan.
In the same skillet, saute onions for about 5-6 minutes until they become tender. Add in the garlic and saute for another minute until fragrant. Pour the onions and garlic over the roast.
Loosely cover the roast with foil or a roasting pan lid. Roast for 2-3 hours, or until the inside of the roast reaches 125 degrees for a medium-rare cook.
Let the roast rest at room temperature for 15 minutes before slicing and serving.