Firstly it displays incorrect losses related to yield which simply aren't applied. Secondly all the emblematic district based bonuses aren't applied to the tooltip. The "losses" are usually just transferring exploitation yield to district yield.

So both an overestimation of the yield losses and an underestimation of the gains happen. This is such a trap for new players. For example one might think that you should never build on rivers, because of all the projected losses. But in fact most (if not all) those displayed losses aren't actually applied.