IMO, as a rule, the closer you can get your feet to the ski, the better (and barring something really unusual, they should both be the same height). Andy cutting out the footbed is obviously the extreme example, but shows how important he thought it was. The basic idea is that less material between your foot and the ski improves your "connection" and ability to control the ski.
With any binding setup, there are trade-offs, so Andy moving to a Reflex was an improvement at the expense of raising the foot. Many skiers have done well with the old HO Animals that raised the foot considerably, and the Goode Powershells, that raise the foot approx 3/8" over a similar Reflex setup.
If someone got creative and designed a realistic way to reduce the material thickness of a hardshell setup, I will wager the performance improvement will be quite noticeable.