Hosting packages on your custom domain via Scarf has no impact on your existing users; your domain adds a new path for users to download your package. You can encourage end-users to switch their pull commands over to your new domain, but they can continue pulling directly from your registry provider with no negative impact.
Should you decide to switch registries later on, current users will have to update their pull commands to either your custom domain or to the new registry URL. If they go straight to the registry, they would need to update every time you decide to switch registries. If they use your custom domain, they will never need to update it again.