We build on WooCommerce for our own D2C brands as well as for clients, which means the problems we solve are ones we have paid for ourselves. Merchant Center rejections, review thresholds, shipping surprises that kill conversion at the last step, COD orders that never complete. These are not theoretical.
The reason we recommend WooCommerce over a hosted platform for brands that need anything unusual is simple: on a hosted platform, checkout is where you discover the ceiling. Everything up to the cart is configurable and then the one thing you actually needed to change is locked. On WooCommerce it is code, so it is a decision rather than a limit.