Not sure if yours is the same as ours but the key is the recalculation. The vnav path is like the Alt cap scenario. The computer comes up with a vnav decent profile at top of decent using the info available to it (current wind, its version of the standard atmosphere ect..) this is why you sometimes see it shifting as you approach TD, its recalculating the descent profile. Once your on the vnav decent it becomes fixed, hence the speed increasing or decreasing as it tries to keep its notional glide path. When you now put a direct to into the box it recalculates the vnav profile , again using its version of the standard atmosphere,current wind and the decent restrictions you put in the box. And so it can now say you are 2000ft high or low. Now weather that agrees with your mental model would be a topic of some discussion!
Good luck with the course!