>you can have a number of sites that use separate domains but are owned by the same entity
Why is this even a thing? There's nothing wrong with storeA.shopify.com, storeB.shopify.com... The only valid use case is if you're somehow trying to hide the shared ownership/platform, in which case it's up to you to deal with the downsides.
AFAIK there are big security risks on hosting user generated content on the same domain of your parent website. That was the main reason github.com migrated individual repo pages to github.io [1]. Also shopify doesn't serve their shops on the domain of their main website, they use *.myshopify.com, I suppose for the same reason.
Why is this even a thing? There's nothing wrong with storeA.shopify.com, storeB.shopify.com... The only valid use case is if you're somehow trying to hide the shared ownership/platform, in which case it's up to you to deal with the downsides.