How does Drupal Commerce use the commerce_line_items field?
This answer refers to the Drupal 7 version, but I assume it's similar for D8.

The commerce_line_items field is a field of type commerce_line_item_reference (basically a reference field) that is defined and instantiated inside the function commerce_order_configure_order_type, in the file commerce_order.module. 

This field of unlimited cardinality stores references to each of the line items in an order. Think of the line items as basically each of the "lines" in an order or invoice that reference a specific product, its quantity, price, and total price etc. 

The values of the commerce_line_items field are initially set in the commerce_cart.module file, inside the commerce_cart_product_add function (basically when you add a product to the cart), in line 1377. 

All of this information can be glanced by studying these files.   

[EDIT]

I'm not sure I'm understanding where you are going with this question, but given your recent edition, yes, you can access the values of the line items by using, for example, an entity_metadata_wrapper, which will allow you to navigate the relationship to each line item and all its fields and properties. See this tutorial for entity_metadata_wrapper