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If the Atlassian App uses our Connect system to integrate with our products, then they do not take up a Jira/Confluence license.
Product Manager, Identity, Atlassian
Atlassian Connect is the way that developers can hook into our products: https://developer.atlassian.com/cloud/jira/platform/integrating-with-jira-cloud/
I guess a better answer is:
If it's some sort of automation that uses Atlassian approved APIs, then there should be no additional Jira/Confluence product license needed.
If it's a script and/or it requires a user to be added to an atlassian product, even if that user is controlled via a script, then that user will take up a Jira/Confluence license.
It really depends on what you mean by Bot, i.e. how it's built / what it's doing.