Preheat oven to 350℉. Prepare 12 muffin cups with paper liners or nonstick spray. Combine milk with lemon juice and let sit 5 min and set aside until ‘curdled’.
In a large mixing bowl, combine almond flour, coconut flour, xanthan gum, baking powder, brown sugar, cinnamon, nutmeg, and a pinch of salt. Combine well with fork making sure there are no clumps. Set aside.
In a small mixing bowl, beat eggs and add about 3/4 of the orange zest, the melted butter, and milk. Pour into dry ingredients and mix well with fork or whisk. Add chopped apple and raisins, stirring to combine evenly.
Divide batter among prepared muffin cups. Bake for 20-25 min. Remove from tin and let cool completely.
While muffins are baking, mix cream cheese, butter, powdered sugar and cinnamon in a small mixing bowl with electric mixer until creamy. Pipe icing onto cooled muffins in the shape of a cross. (Use either an icing bag and tip, or a plastic bag with one corner snipped off.) Top with remaining orange zest.
Notes: To make paleo, use coconut oil instead of butter, use non-dairy milk, substitute honey for sugar, and omit frosting.