Why does my P&L differ from Shopify's numbers?

Because they answer different questions. Shopify reports what was ordered, in customer-facing figures that include VAT and often exclude refunds issued later. A P&L reports what the business kept, which means tax out, refunds on their own days, and every cost that the order caused.

The gaps are predictable rather than mysterious: the tax rate, the discount treatment, the refund timing and the costs Shopify has no field for. Once you can name them, two reports disagreeing is information rather than an error.