hokiefyd 

Many people don't like setting their bike up this way because it does reduce some of the stem's stability, which is probably even more critical with carbon steer tubes. With the stated scenario above, some would remove a spacer from below the stem, and install it above the stem instead. This ensures that 100% of the height of the stem clamp area is clamping steer tube, and the spacer above the stem gives enough compression clearance for the top cap. If one wanted a certain handlebar position, then a stem with a higher angle could be used to compensate for the lower mounting height.

I usually set my threadless cockpits up as you describe above, but I typically use shorter stems (which reduce leverage on the steer tube) and I don't own anything with carbon. All of my steer tubes are steel, and I imagine steel is much more resiliant and forgiving of this type of thing.