PROBLEM
Face dots are invisible, yet if you enable x-ray mode and want to use the box selection with subtract mode, it seems that Blender still uses the dots to determine whether a face is selected or not.
SOLUTION
Blender should make up its mind and either:
- Bring back face dots for x-ray mode
- or detect which edges the box selection encompasses/cuts across and use those to determine if a face is selected or not.