I have been trying to find a solution for keeping track of inventory when a customer orders one of our bundles that consist of multiple items of the same product.
Ex: We sell a 1 box of caffeine gummies and then have variants of it in the form of 2 boxes, 3 boxes, 4 boxes, etc. The bundles have discounts associated as you purchase more. But when a 3 box gets ordered it only subtracts 1 item from the inventory and not 3.
Can this be done natively in shopify yet, and if so, how? And if not, why?
You can't do this with Shopify natively so you'll need a third party solution. Trunk can help you out with its bundling/kitting feature: https://go.trunkinventory.com/helpbundles