How can I configure a free shipping discount for all the bundles?

By default, the total price of the Frequently Bought Together items is the same price as if they were purchased separately.
However, if you want to encourage your customers to buy the full bundle, you can configure different types of automatic discounts, including a free shipping discount.
In order to configure it, just go to the app preferences page and look for the 'Discounts' section:

Once inside, check the 'Apply a global discount to all Frequently Bought Together bundles' option and select the 'Free shipping' discount type:

Then, on the left side, you can configure the minimum bundle amount to apply discounts (zero if you want the discount to apply to all bundles). On the right side, you can also configure the discount message that will be displayed in the Frequently Bought Together widget, and the discount applied message that will be displayed in the shopping cart when the discount is applied. If you want to configure the styling of these messages, it can be done in the 'Visual preferences' section.

The discount won't be displayed on the shopping cart page (this is a Shopify limitation). To overcome that, you can configure a message that will be displayed on the cart page when a discount is applied. You can configure the message, its position and styling, in the 'Visual preferences' section. Also, you can use different placeholders to add dynamic content to this message. For more information, check the related document 'How to show bundle discount information in the shopping cart'.

Important information

The free shipping discount feature provided by the Shopify Platform is quite loose. You cannot limit it to some particular products or number of products so  the only constraint is enforced is the minimum order value.
For that reason, once a free shipping discount is applied to the shopping cart, it would still be valid even if more items are added to the cart or the items in the cart are modified, as long as the minimum order value is reached.
We do our best to check when the cart contents do not match the discount criteria but we cannot cover all possible situations because the cart can be modified by the theme code or other apps and the Shopify Discount module does not enforce strict restrictions on discounts.