Can I show items with this extension in an upsell block only if up-sells haven’t been specified manually in magento?

Yes, it’s possible since with the module you can choose whether to replace manually specified products with the items customers also viewed or not. There are 3 available modes:

• Replace manually added products (the module will replace all manually added items with the ones generated automatically);
• Display manually added products only (only products manually assigned as up-selling will be displayed);
• Append to manually added products (both manually added and automatically generated products will be shown).