Customers with SSO enforced need to first enter the email address on the Atlassian login screen for Atlassian to redirect them to the IdP login screen where they will need to re-enter their credentials. 

Microsoft has a Primary Refresh Token feature that allows SaaS products to authenticate users seamlessly if they are already authenticated on a trusted machine. Primary Refresh Token (PRT) and Microsoft Entra ID - Microsoft Entra ID

Request for Atlassian to support PRT for a more seamless login experience.