Be sure to record your product variant costs in Shopify so that Better Reports can compute your Cost of Goods Sold and Gross Margin accurately.
If the product cost is unknown, Better Reports cannot compute COGS. In such case, the built-in formula assume that COGS is equal to Net Sales, resulting in a 0% margin. As a consequence, your COGS is overstated and your gross margin is understated. This is an arbitrary choice, used as a conservative measure. You could easily create your own COGS and Gross Margin measures to achieve a different outcome. For example, your formula might assume that, if the product cost is unknown, the gross margin should be set to 10% arbitrarily.
A cost of $0 is not the same as an unspecified cost. A cost of $0 means your COGS is $0 and therefore your gross margin is 100%. This is often the case for digital products (an eBook for example).