Hi,
Your topic subject is interesting. It actually defines exactly what the "bundled products" feature does:
You create product A, product B, product C, each one with its own stock.
And then you create product D and in its "bundled products" setting, you can select product A B and C with the quantity of A B and C in product D.
Then, when you want to add to the cart product D, the system will take into account the stock of product A B and C (and the stock of product D if it's not unlimited). And when you purchase product D, it will update product A B and C according to the quantity of A B and C defined in the "bundled products" setting.
So if you set a quantity of 10 in product A, and you add it to product D as a bundled product, you enter a quantity of 2, and then the customer purchase 3 product D, the quantity of product A after the purchase will be 10 - 2 * 3 = 4.
So using that capability, you could create a category of boxes where each combination of wine would be a product and then add the corresponding products as bundled products in these box products so that when the customer purchase one of these box products, the corresponding quantity would be updated in the original products.
The limitation of the bundled products feature is that you can't configure bundled products in variants of products. If you could, then you would be able to link the stock of each option choice to the corresponding product in your "Case of wine - options v2" product directly, without having to create one product for each combination box.
So that could be something to improve in the future.