Why is the delivery cost of auto-charging subscriptions charged separately from the rest of the cart?

When one-time purchases and subscriptions are in the same delivery profile, coming from the same location, and you don't have any specific charge dates set in the subscription rule, then shipping for one-time purchases is calculated with the subscription purchases. But if not, the shipping costs will be calculated separately.
This is one of the limitations of Shopify Subscriptions and you can read about it here https://shopify.dev/apps/subscriptions/shipping-delivery#shipping-rates-displayed-at-checkout.