Units with abilities on their datasheets that allow them to be set up somewhere other than the battlefield must still be ‘set up’ in that locale, and so still count as a deployment choice. When you choose to set up a transport, declare what units (if any) are embarked inside – these are not separate deployment choices.
For example, two players are deploying their armies for the Only War mission. The mission instructs them to alternate deploying their units. Player A starts by setting up a unit of Ork Boyz on the battlefield. Player B then sets up a unit of Intercessors on the battlefield. Player A then sets up a Battlewagon on the battlefield – as it is a transport, Player A declares it will start the battle with a Warboss and a unit of Tankbustas embarked inside. Player B then sets up a unit of Terminators, but uses their Teleport Strike ability to set them up in a teleportarium chamber instead of on the battlefield. Player A then sets up their next unit, and so on.