And they can actually give you lower rates than 2.9% if you pay a higher subscription fee. Stripe won't drop below 2.9% unless you do $1M+ and even then it's not a guarantee.
They provide me with 1.4% + $0.24 for European cards which is a whole lot less than even national banks offer me...
... don't they use stripe as their shopify-branded processor?
Yes but their contract with Stripe let's them give you lower rates. The catch is that Shopify's API can't be used like Stripe's API to handle payments, you're locked into Shopify's checkout page. If you get Shopify Plus ($2000+/month), you can use Shopify's API akin to Stripe's API and accept payments without using the Shopify checkout page.