No, they don't take up an FOC slot -- however, a Dedicated Transport bought for a Troop is a Troop, and a Dedicated Transport bought for a Heavy is a Heavy. For the purposes of the standard missions, this only makes a difference in two missions: Big Guns Never Tire and The Scouring. In these missions, vehicles are scoring (as long as they are Heavy or Fast), so DTs bought for these units would also be scoring (but not denial). It also means they are worth 1 VP in these missions.
Edit: added clarification.
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