Yes, Confluence User Management can still be delegated to JIRA user directories, even if the two applications do not have equal user count license. We just need to make sure that users belong to the correct groups.

Things to take note:

1. Make sure that users that should only able to log in to JIRA belong to the correct JIRA only groups (such as JIRA applications System Administrators, JIRA applications Administrators or JIRA applications Users). Make sure that they do not belong to any groups that are granted "can use" permission is Confluence (for example, Confluence-users and Confluence-administrator group)
2. In that sense, make sure that users that should only able to log in to Confluence belong to the correct Confluence only groups, and are not a member of any JIRA groups.
3. Users that should be able to login to both Confluence and JIRA should belong to both Confluence-related groups and JIRA-related groups. 

Here's a documentation on how to add users to groups in JIRA side:

• Modify group membership

A little about Licensing in Confluence and JIRA respectively:

Licensing in Confluence

License in Confluence is counted towards users who are being given the "can use" permission. You may check this from Administration Console > Global Permissions. This permission will enable users to Log In confluence too.

More information about the user count for your Confluence license

• Managing your Confluence License - Understanding the user count for your license

Licensing in JIRA

While in JIRA applications, license count is based on Global Permissions. Users with any of the following Global Permissions and is an Active status will count towards the license:

• JIRA applications System Administrators
• JIRA applications Administrators
• JIRA applications Users.

More information about the user count for your JIRA license

• Manage group access to applications