[nialo]

The simple obvious first guess is, "Shopify makes a much larger margin, so there is more money available to pay for fraud detection"

Or maybe Shopify knows more about their clients or something like that. Regardless, the margins in Stripe's business are pretty thin, so they can't afford to either eat a lot of losses due to fraud or spend a lot of money on detection. It's totally possible that clients who drop-ship things are not profitable on average for Stripe, even if the vast majority of people drop-shipping things are totally legitimate.