Preheat oven to 375°F (190°C). In a 9-inch pie pan, toss shallots with olive oil to coat. Season with salt and pepper. Roast until shallots are deep brown and tender, stirring occasionally, about 30 minutes.

In a large saucepan, combine beef broth and port wine. Bring to a boil and reduce the volume by half, about 30 minutes. Whisk in tomato paste and set aside.

Pat beef dry and season with thyme, salt, and pepper. In a large roasting pan on the stovetop, sauté bacon until golden. Remove bacon and brown beef on all sides over medium-high heat, about 7 minutes.

Transfer the pan to the oven. Roast beef until a meat thermometer inserted into the center reads 125°F (50°C) for medium-rare, about 25 minutes. Transfer beef to a platter and tent loosely with foil.

Spoon fat off the top of the drippings from the roasting pan. Deglaze the pan with the broth mixture, stirring to scrape up browned bits. Transfer to a saucepan and simmer.

Mix butter and flour into a small paste and whisk into the saucepan to thicken the sauce. Stir in the roasted shallots and bacon. Season with salt and pepper.