Thank you for reaching out!
When you set an application’s login to prompt for the Organization, you are essentially modifying the flow of the application to rely on the Organization input from the user accessing them, which take priority over the normal login flow in this case.
Regarding the issue that you’re facing with Home Real Discovery, you might find useful this following Community post where a similar issue was brought up and resolved. More information on Home Realm Discovery can be found on this page as well.
Each application and Organization requires at least one Connection to be enabled in order to function properly. In the scenario where Organizations are enabled for an application, these will take priority over the Connection for the application itself and it will “overwrite” the prior settings of the app.