Preheat oven to 350°F (175°C). Line a baking sheet with parchment paper and position a rack in the middle of the oven.
In a large bowl, whisk together the rolled oats, all-purpose flour, rye flour, baking soda, baking powder, salt, brown sugar, and granulated sugar. Set the dry mixture aside.
In a second bowl, whisk the egg and canola oil until combined and slightly emulsified. Add the peanut butter, honey, and vanilla extract and whisk until evenly mixed.
Pour the wet mixture into the dry mixture and stir with a spatula or wooden spoon just until blended. The dough will be dry and slightly crumbly.
Use about 2 tablespoons of dough for each cookie. Press the portion together and roll into a compact 1-inch ball with your hands.
Place the dough balls 1 inch apart on the prepared parchment-lined baking sheet.
Bake on the middle rack until the cookies are deep golden brown, about 12 minutes.
Remove the baking sheet from the oven. Immediately sprinkle a little fleur de sel on top of each cookie.
Let the cookies cool on the baking sheet for 2 minutes, then transfer them to a wire rack to cool completely.