The user limit is "number of people who can log in". Whether they're customers, employees, my cat, doesn't matter - if they can log in, they count towards your limit.
Can log in is determined by the global permission, and most Atlassian products ship with a default group set up for it. e.g. Jira-users in Jira. Most of us recommend that you use that group for nothing other than "can log in", and use other groups, or roles to determine "customer", "person in project X", "employee" and so on.
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