When selecting the "Show products instead of variants" checkbox in Shopify, it is still possible to see all the variants in the Algolia Dashboard.
This occurs because the setting enables "distinct: true" only at query time, rather than directly modifying the configuration setting within the index.
To ensure items are de-duplicated in all scenarios, such as when setting up rules, you should also enable "distinct: true" in the configuration within your Algolia Dashboard.