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If I have a unit that has taken a dedicated transport, can they elect to begin the game embarked on another (non dedicated transport). For example all my Orks are starting on the board. A unit of meganobs was purchased with a Truk, but because I rolled player 2, may I elect to start in a battle wagon and leave the Truk empty? Or would they have to start adjacent, embark, and then move?

You can deploy any unit in a transport (that can carry the unit, of course).
Dedicated transports are limited in that ONLY the squad they're bought for can deploy in them, aside from that anyone can ride in them.