Say I sell T shirts in 4 sizes and 6 colours, that makes 24 variations. But if I express the colour attribute as a dropdown using an add-on plugin, then I would need only 4 variations, which is more manageable. Ultimately I could have a simple product with 2 dropdowns. The add-on plugin will propogate the customer’s choices through cart, checkout, order and emails.
Add-ons can’t have their own SKU or image. Some add-on plugins don’t allow the individual add-ons to have a separate price but some do. These restrictions may or may not be a problem for your store. But the objective is to have a more manageable number of variations.
You can export your product using the built-in export feature from the product list page. Open the resulting csv in your spreadsheet and delete the rows of the variations that you don’t stock. You can’t mark a row as deleted. Save the spreadsheet and import it. This makes a new product with the changed variations. You’ll want to delete the old product. You don’t need another plugin for this method.
Another approach you could consider is using this free plugin:
https://www.ads-software.com/plugins/woocommerce-stock-manager/
So you would create all variations, then use the plugin to set the stock of the variations that you don’t supply to 0, (quite easy to do with this plugin) and set “Hide out of stock items from the catalog” at WooCommerce > Settings > Products > Inventory
Either way, ensure the number of variations is less than the variations threshold if you want to prevent customers being able to choose an unavailable variation and then getting the unavailable message.