This might not answer your question directly but here is some good documentation on getting started. https://learn.microsoft.com/en-us/mem/intune/apps/apps-add Opens a new window At the bottom of the page there is a "Next Steps" section that might be of more help. Your question does not specify which platform you are trying to have Intune manage the apps for. There are many different ways to add applications depending on the platform and multiple options per platform that the app can be managed through.
I have noticed a couple of apps like Jira and Confluence that will accept login on a mobile device without an intune requirement.
Can someone please point me in the direction of documentation that walks through the process of adding non-microsoft apps to become Intune controlled?