Alternate Hreflang Extension automatically sets alternate hreflang tags for the Product and Categories Pages. All you need to do in this case is to make sure that Product and Categories pages are enabled in Hreflang Tags For field on the extension general configuration page.
Note: In case you have multi-website Magento and duplicated the same product for each website (do not use the same product ID but create different product entities for each website) and want to connect the product pages with the alternate tags there is a separate Alternative Store View Localizations section for each product.
You need to go to Catalog > Products and set the alternate tags for the products you are interested in.
The same works for Magento 2 categories. You define the alternate tags for them only in case the duplicated category has different IDs for different websites.