Combine flour, oats, coconut sugar, turbinado sugar, cinnamon, nutmeg, cardamom, and salt in a food processor. Pulse until oats are partially chopped and ingredients are combined, about 10 pulses.
Scatter butter pieces, ¼ cup of pepitas, and vanilla over top of flour mixture. Process until mixture clumps together into large crumbly balls, about 30 seconds, scraping down sides of bowl halfway through processing. Sprinkle remaining ¼ cup pepitas over topping mixture and pulse until just combined, 10–15 pulses.
Pack topping mixture together into a ball then break into ½-inch chunks (small crumbly bits are OK) on prepared baking sheet in a single layer.
Bake topping on middle rack until chunks are brown and crisp, 25–30 minutes, rotating pan halfway through baking.
While topping is baking on middle rack, bake apple filling, covered with foil, on the lower rack for 40 minutes.
Remove foil from baking pan, stir apples, increase heat to 375°, and continue baking until juices are bubbly and thick and apples are tender but not mushy, about 40 minutes more.
Spoon apple filling into bowls, sprinkle oat topping over filling and top with ice cream.