That's its own advantage for some people. It means you can sell in countries the US has trade restrictions against, integrate your shop with your WordPress site and modify the source code to your heart's content. Can't really do that with Shopify.
As for the hosted platforms? Eh, I guess like with anything, the market is still big enough for multiple players, even if one of them has a huge percentage of it overall. Google Cloud Platform, Microsoft Azure and Rackspace still manage to do well, even if AWS has more users. GitLab still exists despite GitHub having far more of the market. Etc.
WooCommerce, Magento, Spree, etc. are often chosen for customizability, since Shopify doesn't always serve every need (even with apps). And for control over the platform.