Blend yogurt, apple butter, date, miso paste if using, vanilla extract, cinnamon, cardamom, salt, and soy milk until fully smooth.
Pour the blended mixture over chia seeds in a container and whisk together. Let sit 5 minutes, whisk again to break up clumps, then cover and refrigerate for at least one hour.
Pulse oats, walnuts or pecans, dates, and a pinch of salt in a mini food processor until crumbly to desired texture for the crumble.
Heat a sauté pan over medium-low heat. Add apples, maple syrup, cinnamon, water, and a pinch of salt. Stir and sauté for 3-4 minutes, adding water as needed until apples soften and liquid reduces.
Assemble pudding by dividing chia mixture into 3 jars. Top with cooked apples and sprinkle crumble over. Serve optionally with extra apple butter and maple syrup.