there are two holes so that they dont have to make 2 different parts (left+right). you're stuck using the bottom hole. the link wont fit in the control arm the other way, unless you cut it up.
as for the bolt sticking through the floor, let it happen lol. its just sheet metal. mine punched holes in the floor years ago.
if you actually care, you could just cut down the shank or buy a shorter one.
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