Is there a way to ensure that the number of items available is not affected by the product options? For example, when a product has a set amount of stock, but the options include variations such as additional items, it can show low stock for one option even when there’s ample stock available across other options.
No, and I think is better not to rely on them. Set them low and monitor them every few days (for some reason sometimes it could sell more than the stock you set, etc)