Resolution:
Yes. It is a requirement that the registry entry must be edited.
Without editing it the Agent will not be able to connect to the
CORRECT repository to extract run-time configuration. These values are not set during installation since typically the
values are not known during installation or they can change after
installation.

Here are the examples to edit the registry:

tdagent -editargs -system:repourl tibcr://siebelDemo -system:configurl siebel/example/pubtestagent

You can use this command to view the registry: tdagent -listargs

Note:  Whenever you need to connect to a different Repository Instance or a different configuration, you need to edit the NT Registry entry to reflect how the Agent can startup correctly.