Yes, Vendor add-ons are a separate license from your Atlassian license which you should be able to purchase directly through the add-on. It will show up as a separate line item in your billing page.
Or possibly directly through your Atlassian or partner Account Manager. Especially, for large user base.
Just to add, the number of licenses for the app has to correspond to the number of licenses that you have for your Atlassian product. You can read more about it here in this FAQ.
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