Preheat your oven to 350°F (175°C). Lightly grease a 9x13 inch baking dish with butter or non-stick spray. Optionally line with parchment paper for easy removal.
In a medium mixing bowl, combine the yellow cake mix, softened butter, chopped pecans, coconut flakes, and 3 eggs. Beat together until thick and well combined. The mixture will resemble a thick cookie dough — this is correct.
Press the crust mixture evenly into the bottom of the prepared baking dish using your hands or the back of a spoon. Aim for a consistent, even layer.
In a separate bowl, beat the softened cream cheese until completely smooth with no lumps. This step is critical — any lumps now will remain in the finished topping.
Add the sifted powdered sugar, 1 egg, and vanilla extract to the cream cheese. Beat until you have a thick, glossy mixture that falls off the beater in a slow, steady ribbon.
Slowly pour the cream cheese mixture over the crust layer and spread with a spatula all the way to the edges, ensuring the entire pecan-coconut base is covered.
Bake for 24–26 minutes, or until the top is a warm golden brown. The center may look slightly soft when removed from the oven — this is normal and will firm up as it cools. Start checking at the 22-minute mark.
Allow the cake to cool in the pan for at least 30 minutes before slicing. For clean, picture-perfect squares, wait the full 1 to 1.5 hours until completely cooled. Cut into 12 generous squares and serve.