Yeah, the master variant records some variant-y stuff for products that don't have variants. Consider prices (but this extends to most data associated with variants):
• For a product with multiple variants, they all need prices
• For a product with "no variants" (a single purchasable SKU), it still needs prices
Having a master variant gives us:
• For a product with multiple variants, a place to store the "default price" (the price that might show on a product listing page or a product display page before the customer selects a particular variant)
• For a product with "no variants" (a single purchasable SKU), it gives us a place to store the purchase price for that SKU
All of this means that prices are always associated with variants, not variants and products. This is a little unintuitive, but in the end it makes the system a little more flexible while avoiding the complexity of a polymorphic association.