Yes, you can merge them, but it's not a lot of fun. Whilst "project import" works well there's no way to import the required configuration natively. There are some very good add-ons to do the config import though, and I can't recommend them enough (having done it manually so many times, Botron and Awnba really are worth every penny)
This was the response from Atlassian.
Thank you for writing to us! Glad to assist you here.
As you know, you can restrict project access by modifying the Permission Scheme as documented in How to restrict project access to different isolated user groups
This has one limitation, however, if you also need to Restrict the Teams ability to see each other, they cannot be granted the Browse User Global Permissions, which limits the ability to use mentions or user picker fields, so some functionality is stripped in this increased security layout to separate user base. From the description, it seems that this is what you would like to achieve. Otherwise, here's a feature request to address this limitation tracked at JRASERVER-7467
So If you also need to separate the user base visibility between your teams with the ability of users in the same teams to still maintain visibility of the users in that team you would want to look into federated instances, to have separation in the user pools:
Hope it helps.
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