@Lucas, this is not a server side problem. It is all about the client. If the merchant changes the prefix, the client-side JS is useless.
So either Shopify informs an App of this change, so the App can then adjust the JS (clunky), or Shopify does away with a feature I bet NO ONE uses. Who really cares what the prefix is. My guess is that its a “You think they might need this, but they really don’t” legacy.