I'm using Jira Service Desk (JSD) and Jira Software (JS) in one instance. My Project in JS set to be available for browsing (read only) for Group "Anyone" and therefore public in our internal network whenever you have the link to the issue (internal transparency). Additionally browsing is also allowed to JSD-Portal-Users.
Users can submit requests by sending issues via mail or customer portal to JSD project in the same JIRA instance. When they're logged in, users are always passed to the customer portal page.
As soon a User (in terms of a JSD portal user, not an JSD agent) is logged in, he can not access a link to a (public available) JS issue. He is always passed to the JSD customer portal.
As soon the same User logs out from JSD, he can access the JS issue link.
Furthermore the logged in JSD user can not see his open issues, when he's clicking on the menu item (upper right corner). He's also passed to the JSD customer portal page.
