Pat the chuck roast dry and season all over with 2 teaspoons kosher salt.Heat a large Dutch oven over medium-high heat. Add avocado oil. Brown the beef in batches be sure you don’t overcrowd the pan. Sear on all sides until deeply golden, about 10–12 minutes per batch. Remove and set aside.
Lower heat to medium. Add 2 tablespoons butter to the same pot. When the butter melts, add the onions. Stir in the butter. Reduce the heat to medium-low and add sugar, water and 1/2 teaspoon salt. Cook slowly, stirring occasionally, until soft and golden brown, about 10–15 minutes.
Push the onions to the side of the pan and increase heat to medium-high. Add mushrooms cut side down in the pot. Cook undisturbed until brown and their moisture has evaporated, about 5–7 minutes. Stir with the mushrooms.
Add carrots and celery. Cook for 1-2 minutes. Stir in garlic and cook for 30 seconds, just until fragrant.
Carefully pour in the brandy or cognac. Scrape up all the browned bits from the bottom of the pot. Let it simmer for 2–3 minutes to cook off the alcohol.
Return the beef to the pot. Add broth. Stir in thyme, bay leaf, and soy sauce sauce. Stir to combine. Bring to a gentle simmer. Cover cook on low for 1 1/2-2 hours, or until the beef is fork-tender. Remove thyme stems and bay leaf.
If making a pie crust, while the beef cooks, make the pie crust and prepare the thickener: Whisk in ⅓ cup flour with 1/2 cup beef broth until smooth. Divide dough into two portions—one for the bottom crust and one for the lattice top. Chill until ready to use. When the beef is tender, slowly stir the flour and broth mixture into the simmering filling. Bring to a boil and reduce to a simmer. Stir frequently to avoid sticking until the beef mixture is thickened and glossy. The filling should be rich and stew-like, not watery. Add remaining tablespoon butter. Stir until melted. Let cool slightly before assembling.
Lightly grease a 9-inch pie plate with non-stick olive oil or avocado spray. Preheat oven to 425 degrees.
Roll out bottom crust and place into pie dish. Fill with slightly cooled beef mixture. Roll out second crust and cut into 2-inch strips. Weave into a lattice over the top. Trim and crimp edges to seal. For a shiny, golden finish, brush the top with beaten egg.
Bake for 15 minutes. Reduce the heat to 400 degrees and bake another 20-25 minutes until crust is golden brown and filling is bubbling through the lattice. If crust browns too quickly, tent loosely with foil. Let rest 15–20 minutes before slicing so the filling sets.