It appears that the yield changes you can see in a "Build Improvement" tooltip will always show currently active yield change modifiers on the plot tile as projected additional yields. The easiest way to see this is by playing as Mansa Musa and building a mine on a copper tile. Then hover over the Build Farm action, and it will say: "+1 Food, +4 Gold". The +4 Gold is Mansa Musa's trait modifier for mines, however this modifier would obviously no longer be valid once a farm was built on the plot instead of a mine (not possible in vanilla of course, but well within the capabilities of mods). While it is indeed difficult to calculate what the yield change would be if one improvement was build instead of another one that is already present, I don't really see why current modifiers should be included in a tooltip that is supposed to show a projected change.