PASSED Manual Testing following the steps in the description.
Tomcat 7.0 + MySQL 5. Portal 6.2.x GIT ID: 810f663e5ac7010c8e5aa6ed903d7971a6d190cc.
User was able to see explicit organizations only (ie Org2 and Org3). And the search results for all organization which are members of Site1 also return Org2 and Org3 only.
Tomcat 7.0 + MySQL 5. Portal 6.2.x GIT ID: 6f19942f4cd08558e83ef9a52f0950347135940c.
User is able to see all organizations listed which are members of Site1, including implicit Org1. And for the implicit one, a help message is displayed to explain why this organization is shown here even if we haven't assigned it manually.