I like to carry my bikes upright inside my vehicle (with the front tire removed and the fork clamped to the floor). They don't get damaged and are less likely to get stolen inside the vehicle (I have a cable lock that will slow the thieves down a bit more). I can go inside stores, hotels or take a hike without much concern for theft.

I currently use a Isuzu trooper which has tremendous floor to roof height for even my tall framed bikes. But I am nearing the end with this vehicle so I'm beginning to look at new vehicles and am frustrated with how manufacturers list interior dimensions. They always give them in cubic inches which doesn't help me. I need dimensions for floor to roof heights and rear door openings.

One thing I have found is that if they hang the spare tire on the rear door, it usually gives you more interior height as not doing this means the spare tire is usually under the floor.

Having a quick release seat post clamp allows you to drop down (or remove) the seat for more clearance.

Measure your bike(s) and bring a tape measure with you when you shop for vehicles.