I personally think it has to do your body's inertia during shifting and the "ergonomic speed" in which gears need to be shifted up or down. I don't think manufacturers are arbitrarily choosing one way or the other. One way should be better for driving from a motion analysis perspective. This applies less to paddle shifters or putting around town but here it goes:
During acceleration, your body weight is shifted towards the back.. it is more controllable to be holding and/or pulling the gear lever, instead of trying to push it (as g-forces are already working to make it harder for you to reach and push things in front of you).
During braking, your body weight is shifting forward.. it's more controllable to keep pushing the gear lever forward to downshift (g-forces in this case helping you maintain contact with the gear lever).
Also, cars typically decelerate quicker than they can accelerate, meaning there is less time to perform downshifts versus upshifts. It seems easier and quicker to push/punch the gear lever to downshift -- you don't need to wrap your fingers around the lever to push/punch it, saving motion and time.