Hello @Ankush Gurjar,
Thank you for posting your query on Microsoft Q&A.
Based on your description, it seems you have developed a custom application and are trying to configure Single Sign-On (SSO). When you created the application via App Registration in Azure, you noticed that there was no option to set up SSO. However, when you created the application through Enterprise Applications, you were able to configure SSO.
This behavior is expected. SAML Single Sign-On is not available when you create an application through App Registration. The correct approach for your custom application depends on the protocols it supports. If your application supports the SAML protocol, you should create the application through Enterprise Applications and configure SSO. However, if your application supports OAuth or OIDC protocols, you need to create the application through App Registrations.
I hope this information is helpful. Please feel free to reach out if you have any further questions.
If the answer is helpful, please click "Accept Answer" and kindly upvote it. If you have extra questions about this answer, please click "Comment".
Thanks,
Raja Pothuraju.