Can we get confirmation on whether or not the cargo specifications are related to the ship's internal cargo bay, and whether or not the Starfarer Gemini's cargo size is reduced due to the increased mass of armor?

The numbers provided for the Starfarer and Starfarer Gemini are the aggregate of their internal and external cargo capacities. Most of the cargo reduction on the Starfarer Gemini is because of changes to the internals, where it will mount more reinforced bulkheads and larger military-related equipment.