Can I exclude one tagged product from the Frequently Bought Together recommendations but not from Also Bought's?

If you have both Also Bought and Frequently Bought Together installed in your store, a product tagged as Hidden recommendation will be excluded from both apps recommendations.

If you only want the product to be excluded from the Frequently Bought Together recommendations, you can tag it with the exact text Hidden FBT recommendation

This tagging can be done in the Shopify product editing page: