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I received this answer from one of engineers.
Speaking for Exalogic verify-topology I can state that EL v-t only verifies the factory cabling specifications for each of the three factory configurations (half, quarter, full). As soon as you change the cabling configuration such that it is no longer per the factory specification, you should expect the current v-t to fail. It is my understand that when you cable racks together, you do indeed disconnect certain point to point connections that v-t expects to be there, and you also introduce new connections that v-t will not check.
In EL-ED multi rack configurations (and for all other InfiniBand fabrics) you can run ibnetdiscover to check the topology manually and ibdiagnet to perform diagnostics.