I think another large part of it is that we can't take into account the actual emissions before they happen. In some cases emissions have increased rather than decreased.
We can estimate how much methane will be released by thawing permafrost but we can't know for sure until it happens, we can estimate how much CO2 will be absorbed and released by seawater every year, but that can change based on environmental factors and saturation.

I also wonder how much pressure is put on climate scientists by governments to under report or misrepresent findings.