Preheat your oven to 375°F (190°C) and line a 12-cup muffin tin with paper liners or generously grease each cup.
In a large bowl, whisk together the all-purpose flour, baking powder, salt, dried thyme, and black pepper until evenly distributed.
In a separate medium bowl, whisk the eggs until lightly beaten. Add the milk, olive oil, and honey, then whisk until thoroughly combined.
Toss the diced apples with a teaspoon of the dry flour mixture. Mix the shredded cheese with the chives and set aside.
Make a well in the center of your dry ingredients and pour in the wet mixture. Stir gently with a wooden spoon or spatula until just combined—about 10-12 strokes.
Add the floured apple pieces, 1 cup of the shredded cheddar, and nuts (if using) to the batter. Fold gently with a spatula just until distributed.
Using an ice cream scoop or ¼-cup measure, fill each muffin cup about ¾ full. Sprinkle the remaining cheese, oats, and a tiny pinch of flaky sea salt over each muffin.
Bake in your preheated oven for 22-25 minutes, or until a toothpick inserted in the center comes out clean and the tops are golden brown. For the most even baking, rotate the pan halfway through the cooking time.
Allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack.