Preheat the oven to 350 F and line a 9 x 13 inch pan with parchment paper.
In a large bowl, mix the flour, sugar, and ground flaxseed together, then add the butter in 1 Tbsp chunks and rub the butter with your fingers into the dry ingredients until the mixture resembles fine breadcrumbs. Knead the mixture a bit until it clumps together, then pat evenly in the base of the baking pan. Bake for about 20 minutes until just browning.
While the crust is cooling, combine the butter, brown sugar and sweetened condensed milk together in a pan over low heat. Once the sugar is dissolved, gradually increase the heat to medium-high to bring to a boil while stirring continuously. Do not stop stirring, even briefly. Once the caramel is boiling, turn the heat down to low and continue stirring for five minutes until the sauce thickens. Pour filling over the shortbread crust and spread evenly.
Sprinkle the pecans, then pumpkin seed and sunflower seed evenly over the caramel filling. Sprinkle the chocolate chips on last, then lightly press the topping into the caramel with the bottom of a measuring cup. Replace in the oven and bake for 20 minutes to set the top. Remove from the oven and cool. Cut into 2.5 x 3 inch pieces, 15 per pan.