I think there's some confusion here. This topic is about developers selling apps via the Shopify App Store, not about how much you pay Shopify to run an online ecommerce store.
Shopify charge a monthly fee for their online ecommmerce stores, and they don't take a 20% cut for that.
I've been really enjoying SpreeCommerce (based on Rails). You can get away with very little coding if you're happy with the current feature set (which really covers all the basics and then some) and your Payment Gateway of choice is supported by them already or within the ActiveMerchant Payment Gateway options. And then writing your own Payment Gateway integration (like for offsite payments) is really easy too.