How do I programatically generate multiple "add to cart" forms on product display?
I implemented this through patching Commerce Add to Cart Extras. My patch can be found here: https://www.drupal.org/node/1836200

In brief, the line item type contains a reference to an entity, a field collection item, actually.

I used views to generate a list of products with an add to cart form using Commerce Add to Cart Extras, joining (by a views relationship) on my field tables that provide the reference which must be attached to the line item.

Next, I had to alter Commerce Add to Cart extras so that the views result containing my entity id which must be added to the line item will copy that id over to the line item when the line item is created.

In the end, I have a list of multiple instances of the same product with a quantity field and a single add to cart button. Each product has the entity which must be added to the line item. When one of those products is added to the cart, the entity id gets copied over to the line item.