I can see how the concept of stacking and separation may seem at odds with each other from the unacquainted perspective.
Separation is the mechanism we use to achieve being square and being stacking as well as the mobility we use to convert stacking from apex to apex and to covert being square from transition to transition. Even when we are “square” to the skis and all of the rotary, angulation and inclination are completely neutral, such as in transition, we are still using vertical “separation” through flexion and extension in the vertical plane of movement.
The five fundamental moves of separation are flexion, extension, rotation, angulation and inclination. Flexion and extension provide separation of the CoM and BoS in, primarily, the vertical (when upright) and, secondarily, in the lateral plane (when tipped). Rotary, of course, provides separate and differential rotary orientation of the CoM and BoS. Angulation and inclination provide separation in, primarily, the lateral plane and, secondarily, in the vertical plane.
Skiing is all about the relational displacement of the CoM and the BoS in all four planes of movement which is facilitated by the five fundamental movements of separation. Because being “stacked” or “square” can be considered as the outcome of separation, they are not comparable on the same scale of measurement, whatever that may be.
For me, the CoM and BoS are the two primary loci of control a skier has. When we limit our direct focus on the control of these two facets, the five movements of separation that occur between these two points happen as a result of these two distinct paths. These movements are not directly facilitated by skier intent and are merely movements that we can allow to happen on their own accord and the best way to produce natural movements that are inherent with the DIRT that comes from the ski.