Wake up the yeast. In a large bowl, whisk warm water with honey until dissolved. Sprinkle in instant yeast and let it sit 2–3 minutes. It won't foam like crazy (instant yeast is chill), but it should smell yeasty.
Build the dough. Add olive oil, salt, whole wheat flour, and bread flour. If using Greek yogurt, add it now. Mix with a sturdy spoon until shaggy and slightly sticky.
Knead to smooth. Turn onto a lightly floured surface. Knead 7–9 minutes until the dough is smooth, elastic, and just tacky. If it's gluey, sprinkle in 1–2 tbsp bread flour. If it's stiff, wet your hands and knead moisture back in. Aim for soft and springy.
First rise. Place dough in a lightly oiled bowl, cover, and proof in a warm spot until doubled, about 60–90 minutes. A clear container helps you spot the rise. No sauna? The oven with just the light on works.
Prep the garlic herb butter. In a small pan, combine butter and olive oil over low heat. Add garlic and warm gently 1–2 minutes until fragrant (no browning). Stir in parsley, basil/thyme, red pepper flakes, lemon zest, salt, and pepper. Set aside. The kitchen should now smell like victory.
Divide and roll. Punch down the dough. On a lightly floured counter, divide into 12–16 equal pieces. Roll each piece into a rope 8–10 inches long.
Tie the knots. Tie each rope into a simple knot, tucking the ends underneath for a tidy little bun. Place on a parchment-lined sheet, spaced an inch apart.
Second rise. Lightly cover and let them puff 25–35 minutes until slightly swollen. Preheat oven to 400°F (200°C) while they rest.
Bake. Brush knots lightly with olive oil or a bit of the butter mixture (save most for after). Bake 12–16 minutes until golden with a firm spring.
Brush and toss. While hot, brush generously with the garlic herb butter. Sprinkle with Parmesan, extra herbs, and flaky salt. Toss on the tray so every nook gets saucy.
Serve. Eat warm as-is, or dunk in marinara, pesto, or a lemony yogurt dip. Prepare for people to hover.