Adding option to one product in Commerce but not to others of the same product type
You can build your restaurant menu based on views, where you list commerce_products instead of product types(nodes). This will render one row for each variation. 
You can also add relationship to your product types(nodes) for rendering/grouping/filtering.

You can also render the view of product variations at the product full page. Then the user will see all the possible variations of current product at once.