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By "trunk mount", do you mean mounted on the rear of the car, behind it? (I'm pretty sure you don't mean on top of the trunk lid itself.)
Your goal should be: (1) inside the car, if possible with the trunk closed; (2) rear mounted behind the trunk (not on top), with as many wheels/seats removed and put in the trunk as possible (3) roof mounted.
The problem with roof racks is they increase both frontal area (A) and drag coefficient (Cd), where a rear rack probably only increases Cd (unless the bikes stick out the sides too). So roof racks are a double whammy.
As Daox says, for a rear mount, you want the bikes riding as low as possible behind the car.
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