When there is a mismatch between the user identifier the SAML IdP potentially has for a user and what the Atlassian application is using, the functionality for parsing usernames may be used. Depending on how your organisation's Active Directory (AD) is set up, the username may be able to be derived from the user's email.
Example:
At John Doe's organisation Azure AD is not synchronised with local AD therefore the Azure AD will not have sAMAccountName (i.e. "username"). At this organisation the username can be derived from the user's email e.g. the email is "john.doe@domain.com" and the username is "jdoe". The IdP can be configured to send the user's email address as the user-id, and EasySSO can have a pattern set up to parse it:
^(.).*\.(.*)@.*$
and convert to a sAMAccountName:
$1$2