Problem Definition

When a customer has several separate Cloud instances with different URLs on the same domain, they cannot create and link two separate applications within their Identity Provider as the Entity Provider URL is configured at organization level and not at instance level. Each of the separate applications will have a separate Entity Provider URL.

This disrupts the Identity Provider initatiated workflow as it doesn't allow the customer to create separate applications for each of the instances and manage separately the access to those aplications.

Suggested Solution

Have the option to configure SAML separately by instance rather than by Organization or Domain.

Workaround (Optional) 

When users log in via the Cloud instance URL (Service Provider initiated workflow) the users can still access.