Thanks for reaching out.
Azure's own certificates for SAML SSO feature is not available outside of the GUI. Alternatively, you can use Graph API way assigning custom certificate to the application which is similar to import feature in portal.
More Details:
https://learn.microsoft.com/en-us/graph/application-saml-sso-configure-api#step-4-configure-a-signing-certificate
Regards,
Siva Kumar Selvaraj
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