Can I set one product as a global recommendation for Frequently Bought Together but not for Also Bought?

If you have both Also Bought and Frequently Bought Together installed in your store, a product tagged as Global recommendation will be displayed as a global recommendation for both apps.

If you only want the product to be a global recommendation for the Frequently Bought Together app, you can tag it with the exact text Global FBT recommendation

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