At this moment, the pricing for Jira (both Cloud and Server) cannot differentiate between users that actually use the add-on and users that do not need access to it.
This is why when you install an add-on it is priced for the total number of users that have access to your Jira (except for Service Desk portal-only customers). However, before installing you see the price for your particular Jira site. Also, you can always see the license count for each product (and add-ons) by navigating to the site administration area -> billing -> manage subscriptions.
I don't think this needs is uncommon. In fact the contrary and my company have the same. We have >100 users for JIRA SW but only 10 needs Zephyr and we really do NOT want to pay for 90% of users not using it. This question was raised a year ago. Has Zephyr/JIRA made any change since then?
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