Lee Adama's Viper is damaged after he destroys a missile that targets Colonial Heavy 798 in the MiniSeries. The starliner recovers the Viper into its cargo bay. The cargo bay was also only seen in the MiniSeries. Coincidentally this scene was Jamie Bamber's first day of principal shooting for the Miniseries.
The cargo bay scenes on Colonial Heavy 798 were filmed on the portside lower car deck of one of the V Class BC Ferries at the Tsawwassen Ferry Terminal. Possible ferries used include The Queen of Vancouver, Queen of Esquimalt or Queen of Saanich. In 2002 the V Class ferries were one of the only ferries in the fleet that didn't have multiple rows of portholes on the main car deck besides the Burnaby Class.
The car deck was redressed very little for the shoot. The only noticeable changes are that the signage has been covered and large shipping containers were strategical placed to cover up ferry details as seen in the screen cap.
You can see from this vantage point on the Queen of Saanich photo that the two images are nearly identical.