Is the intrustion for the black tank vent pipe supposed to be sealed on the roof? It's sealed around the cap but the pipe itself isn't. That brown on the inside of the cap is the wood of our roof.
This will get you through, but that pipe is too short now. I would find a smaller diameter pvc pipe that fits perfectly and extend the vent about 6 inches or so. Then put the cap on it. And yes, with no vent cover you will get leaks into the interior.
Source: Black tank vent problem