Yes you can licence each application independently and do not have to have a common set of users. So a user can be only in the 500 for JIRA, only in the 100 for Confluence or in both.
You may like to consider how you will manage these users. For your example I would recommend using JIRA as your Master User Directory and setting your user accounts/groups up in there with a link from Confluence to share. See https://confluence.atlassian.com/display/CONF58/Connecting+to+Crowd+or+JIRA+for+User+Management for instructions on how to connect.
I hope this helps
Since this is cloud you don't have to manage your users. The User Management section of Cloud will handle that for you. But the first paragraph is correct, only users that have access to each application (Jira / Confluence) will be counted towards that application. So you can easily have JIRA Software on the 500 user tier and Confluence on the 100 user tier. The second paragraph is for Server customers.
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