IF they took the front passenger seat out, they would be able to make a ramp from the back door of the Element to just roll into it, as for swapping out of the wheel chair to the driver's seat, I'd have it lowered, it's possible, and you can always buy smaller wheels for it too to get some extra wheel well clearance. It takes quite a bit of parts to lower a car, raising it is easy, just raise it basically, but lowering you're talking about buying all new springs and such. I don't think a Honda dealer would be the best bet at doing that, maybe a custom shop or a good mechanic.
Does this person have the ability to walk or crutch momentarily? I knew a person who keeps crutches in the back of the car, (they only have one leg) puts the wheel chair in the back, when she gets to it, pulls the crutches out and goes to the front of the car to get in.
If they cannot walk at all, you're also talking about hand controls, which is really easy to do on almost all Hondas.