Equinox sunrise sunset direction
Due to the atmospheric refraction the Sun rises earlier and sets later as you correctly wrote. Refraction however is perpendicular to the horizon. So if the apparent sun rise is earlier, than the true (actual) position of the Sun will be more to the north east (smaller azimuth) than when the true sun rise occurs. As refraction is perpendicular the apparent sun rise will also be more to the north east and hence the azimuth will have a lower value (88-89° instead of 90°).

NB. This is of course only true from the northern hemisphere.

NB2. The Sun is not to scale in the figure below.