How can I configure a 'cheapest item for free' 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 'cheapest item for free' discount.
Once inside, check the 'Apply a global discount to all Frequently Bought Together bundles' option and select the 'Cheapest item for free' discount type:
The Shopify Discount system is quite limited. For example, generally no more than one discount can be applied to a single order. On the other hand, the Shopify Platform does not enforce all discount constraints regarding the products in the order. We advise you to review the related document 'Important implications about discounts' before enabling discounts in your store.