Great question!

Shopify will only show one option for subscription shipping on checkout.

Shopify defaults to the cheapest shipping rate available, since it's a recurring cost.

Shopify will NOT show all of your multiple shipping options at checkout for a subscription product.

This is a Shopify limitation.

If you have shipping rules like shipping rates based on minimum dollars spent, weight, Shopify will take all that into consideration when displaying shipping prices for subscriptions.