they come thru the floor about 1/2" at the rear pan. i plan on adding padding to either side of them under the carpet i plan on putting in. this should keep the floor looking level. plus how often do you ever have people sitting in the back seat of one of these anyways. its a bit cramped LOL.
you can use 2" tubing without it coming thru the floor if you do one of 2 things, you either overlap it so it sticks lower than the framerail at the back, or you cut 1/2" out of it on its top side so it just butts to the floor at that spot. both things i think make your install weaker than it should be.
this is why i kept the tubing boxed as far back as i could before opening the top to fit against the rear framerails. this pic i attached shows how i opened up the rear framerail just behind the floorpan for the connector.