Conclusion:
Yes, the additional items that are added to the cart are regular products in your store and are associated with a sku. If you would like for Inventory to be tracked on these upcharge items, it is vital that you set the "Shopify Tracks this Product's Inventory" option on the product its self in the Shopify Product Page. That way, Shopify will keep track of how many of this item you have in stock.
If these products can run completely out of stock, it is important to note that you may have to apply the custom code in the article listed below to prevent customers from adding the main product to the cart if they have selected an upcharge product that is currently out of stock.
https://w3trends.zendesk.com/hc/en-us/articles/236232108-Check-options-inventory-levels