Combine. In a medium saucepan, combine butter, brown sugar, honey, cream, and salt.
Cook. Whisk over medium heat until the mixture comes to a boil. Boil just 3 minutes, whisking regularly. (The surface should look foamy and slightly lighter in color than before.)
Finish. Remove from the heat and stir in chopped pecans and vanilla, stirring well to coat the pecans fully in the salted caramel mixture. (You'll notice the caramel mixture has thickened)
Pour Filling Over Crust. Carefully pour the salted caramel pecan filling out over the baked shortbread crust. Gently use a spatula to spread the mixture (be gentle so the pecans don't dent or scrape the crust!).
Bake at 350 degrees for 10-12 minutes, or until the edges are just set and the center is still slightly wobbly. (This wobbly center is important, since the bars will continue to cook for a few minutes once you pull them out of the oven. If your center doesn't have any wobble at all, the bars may set up more stiff and chewy than soft and gooey.)
Serve & Store. Sprinkle with flaky salt if desired, and let the gluten-free pecan bars cool completely before cutting into squares so the filling doesn't drip. (You can put them in the refrigerator to help speed up this process.)