To avoid hitting a lump of cumulo granitus GPS altitude is more useful. To avoid hitting another airborne moving object pressure altitude is what you need.
Actually GPS height is equally good for terrain avoidance and aircraft separation - assuming everyone is working to a common system. It has in fact been mooted that aviation could, in time, move completely to using geometric height. Not only would this remove the complication of transition altitudes, but could save fuel by avoiding the invisible climbs and descents that are an inevitable consequence of flying through pressure systems. However many aspects of aircraft performance relate to pressure altitude. One could envisage the bizarre situation of aircraft having to request a descent simply as a result of flying into a region of low pressure.