There is no desynchronization happening between the last event and the repaint (that can be verified with Debug.Log of the event position and the element resolved styles top/left inside a generateVisualContent callback). The issue seems to be a deeper level, where the editor has some specific logic to collapse mouse events to avoid invoking UI code at too high frequency. This effectively means that UI is capped at a specific frame rate which is below the speed at which mouse events come in.

One interesting thing to try would be to read the mouse position at the last possible moment before rendering but unfortunately we lack such APIs in the editor. Saving the last seen value from input events will unfortunately not solve this as it will suffer the same delay.