I have been boot fitting a while I know what your saying, but using heel lifts is a very valid fitting aid. I very often build a custom lift onto the footbeds I make. You are correct yes that a footbed is a good starting point, but if you were still getting calf pressure or heel lift for example, then adding a heel lift to the footbed, would be a very viable option.
The main reason I responded in the first place is people saying just get a footbed, without really understanding why it helps. I was trying to explain why raising the heel, be that by using a heel lift, a footbed or both works to help certain problems.