The Notify When Available button works with variants as long as they are selectable (Clickable). The app automatically identifies the products that are out of stock and the button will be displayed only if a customer select the out of stock variant:

A variant Out of Stock:
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A variant in Stock:

If the variants in your store are not selectable, then our app will not be able to show the Notify When Available button based on the variants. In this case, you can either ask your store developer to make out of stock variant selectable or you can enable "Always Show the widget" option from our app. For that, do the following:

Then, our button will display if any of the variants are out of stock; however, when the user clicks on the sign-up button, they will see only out of stock variants to select from the dropdown. So they can subscribe to only those variants they want.