With Atlassian Cloud you don't connect Jira to Azure AD, you connect Atlassian ID system via Atlassian Access.
A user who is trying to access a particular resource (e.g. an issue in Jira Cloud) that requires authentication will be kicked out to the login page, once email is entered if the email domain is one of the verified domains from your organisation, your Atlassian Access configuration will "take over" – if there is a SAML SSO configuration against Azure AD, then the user will be kicked out to Azure AD to perform authentication, and once successful, be returned to the resource. If the email is from some other domain (e.g. a different organisation) – either Atlassian Access of that organisation will deal with the authentication or the default Atlassian ID system will.
As such you don't authenticate to Jira Cloud, you authenticate to the whole Atlassian Cloud and then access one of the instances available to you.
So yes, the answer is "yes".
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