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.
The discounted amount 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 the discount is applied. You can configure the message, its position and styling, in the 'Visual preferences' section. For more information, check the related document 'Why are discounts not displayed in the shopping cart?'.
The Shopify Discount system is quite limited. For example, 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.