Not quite sure if I get what you mean. You have users who bring their own devices and register them with Intune. These users are typical admins on their own devices. They will often use the Company Portal to register, which requires admin rights. The devices themself will show up as Personal in Intune, as opposed to Corporate under Ownership.
As standard users they will not be able to make major changes to the system, such as installing software, the principle of least privileges. One of the many benefits of having these devices in Intune is to deploy apps. You can make them available or required. So in this scenario, these users won't have any need to install any apps. This is automatically handled by Intune. Do I miss something?