User X is a customer for project A, but in project B he is an agent.
When he logs in Jira Service Management (not in the Customer Portal), he can browse both projects, and can see the project A queue (like if he was an agent in Project A, which is incorrect).
He is added into project A with only Customer role, and in project B as Service Desk Team role.
Yes, that is possible. You need to check your permission scheme used by both projects and check who can browse the project. I would recommend that you give project roles browse permissions and make sure the user in question is only set up as a Service Desk Customer in project A and that the Browse permission has Service Project Customer - Portal Access added to it. That way the user would only be able to access project A via the portal.
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