This not solved. HMRC will not accept a spreadsheet just showing the fees taken from each transaction, which is the spreadsheet you get when you download from the Payment screen.
Shopify supply a service by charging a fee to use Shopify Payments, it is for example 2.2% + 0.20p per order.
HMRC requires the following on an invoice for supplying a service.
Your invoice must include:
Shopify use Stripe to process Shopify Payments and we also use Stripe for other websites and we receive a monthly invoice from Stripe which show these charges.
Shopify are in the wrong in not producing an invoice for a service they provide and HMRC will catch up with them.