Preheat the oven to 350°F (175°C). Spread the 2 cups of unsweetened coconut flakes in an even layer on a baking sheet and toast for 3 minutes; stir and toast another 1 to 3 minutes until golden-brown, watching closely. Remove and let cool 5 minutes.
Measure out 1 cup of the toasted coconut flakes for the dough and leave the remaining 1 cup on the baking sheet for coating.
In a medium bowl, whisk together the 1 cup toasted coconut flakes, oat flour, toasted quinoa flour, Dutch-processed cocoa powder, baking soda, and salt until evenly combined.
In a large bowl, whisk together the light brown sugar, melted coconut oil, eggs, honey, coconut (or vanilla) extract, and water until smooth.
Add the dry ingredients to the wet mixture and stir until just combined, then fold in the semi-sweet chocolate chips.
Shape the dough into a log, wrap in plastic wrap, and refrigerate at least 30 minutes, or until it is no longer sticky and is firm enough to portion.
Line a baking tray with parchment paper. Using a rounded tablespoon, divide the chilled dough into 35 equal portions and let them rest 10 minutes.
Form each portion into a ball and roll in the remaining toasted coconut to coat. Place balls about 2 inches apart on the prepared baking sheet.
Bake for 6 to 9 minutes, or until the tops are no longer wet; cookies may crackle slightly. Remove from oven and let sit on the baking sheet 2 to 5 minutes to firm up.
Transfer cookies to a wire rack to cool completely.