SAML and External Realm users are compatible with each other, so existing users will work fine using SAML instead, as long as their username matches up. To modify the username that is received by FlexDeploy, change the Unique User Identifier (Name ID) claim in the SAML provider. No changes are needed in FlexDeploy for this.
Additionally, the email, first, and last name are used if provided in the SAML claims and are used to help setup new users.