Preheat oven to 350 degrees. Line a square baking tin with parchment paper and set aside.
In the bowl of your food processor (or a small bowl), mix together flours, sugar, and salt. Mix in vanilla and egg. Add in the coconut oil and ghee and process until the mixture forms a coarse, gravel like texture that sticks together when pressed
Dump the mixture into the baking tin. Firmly press down on the dough until it even covers the bottom of the tin in one compact layer. Bake for 12 to 15 minutes, or until it is slightly golden brown. Remove from oven and let cool.
Meanwhile, place a small sauce pan over low heat. Whisk together lemon juice, lemon zest, honey, eggs, and egg yolks until completely combined. Add in ghee and coconut oil and mix until they are melted. Turn heat up to medium and continue whisking until small bubbles start to form on the top and the mixture begins to thicken, about 5 minutes.
Remove mixture from the heat but continue to whisk for another minute or so. Pour through a strainer into a bowl to remove any lumps. Mix in the chia seeds then pour over the crust. Refrigerate for at least 4 hours, preferably overnight.
To serve, remove from the tin by lifting up on the parchment paper, then cut into 9 or 16 squares, depending on how many you want.