This is true. Projection systems rarely assume that young players will break out, so I think they are more likely to underestimate than overestimate there.
Conversely, bad teams are likely to lose some veterans after the trade deadline which I don't think projections take into account.
Another mostly unrelated thing I have often wondered about projections is that they almost never project anyone to have a great season because they push everyone towards the mean. This makes them more likely to be right on average. However, I wonder if maybe the projection systems work better for average players than they do for players at the extremes. There are more people in the middle, so there is more certainty in projections. There are so few great players that I think it's harder to get them right.