They can and they will. There is still alot of room under the van. Remember, a black tank on a van is largely above the floor and is that box underneath the commode.
I've seen cassette toilets in truck campers and expedition vehicle. It does offer some flexibility, as well as a moveable, rotating toilet that can make a small space much more comfortable.
The Euro designs usually have more skylights than US vans because they don't have the AC unit up top. So you could still have AC, but you'd loose a skylight.
If you search youtube, you'll see alot of interesting designs. I highly recommend the channels for Practical Motorhome and Motorhome Campervan as a good starting place/repository of van reviews.