It's not necessarily a lack of student buoyancy control or situational awareness that underlies my position. I fully expect to have trained my students well enough that they can stay off the bottom and know what's going on around them. The issues are compliance with PADI standards, the exercise of my professional judgment as an instructor, and student control.
PADI sets a depth limit of 100 feet for any AOW training dive. Although PADI standards do not state that the bottom must be at the depth limit, PADI does require that the instructor exercise sound judgment in selecting training sites. A site where the bottom is still 40 feet below you at the maximum dive depth is not a desirable training site, in my opinion. Or, to put a finer point on it, I know my brethren of the bar can't impeach my judgment for selecting a conservative site.
Student positioning and control is drilled into you as a Divemaster (if you have a good course) and certainly during instructor training. Maintaining control over students is more difficult while floating in the water column away from a reference point. I prefer to have something below my students besides water. It makes my job easier.
Finally, students don't always listen to you.
I understand your point about training students for a "realistic" environment. However, I doubt that in Cave 1 a diver is taken a mile back into the system for initial training because that's where s/he may be diving. In my opinion, training should proceed incrementally. Get the student comfortable with the basics in a carefully selected environment, and then progressively move them forward toward more challenging dives and environments.