In downcut milling, the end mill pulls itself into the workpiece, which can lead to the gantry or the Z-axis beeing pulled uncontrolled (backlash of lead screw) in the direction of the workpiece during the removal of larger chips. This causes a less precise milling pattern and can even result in the breakage of the end mill, if the chip building is too large.
Assuming backlash-free ball screws are used, the downcut is preferred over the upcut milling.